Miracle-dz/UniFAR-FTUs huggingface dataset:
Optimizing experimental design for genome sequencing and assembly with Oxford Nanopore Technologies

High quality reference genome sequences are the core of modern genomics. Oxford Nanopore Technologies (ONT) produces inexpensive DNA sequences, but has high error rates, which make sequence assembly and analysis difficult as genome size and complexity increases. Robust experimental design is necessary for ONT genome sequencing and assembly, but few studies have addressed eukaryotic organisms. Here, we present novel results using simulated and empirical ONT and DNA libraries to identify best practices for sequencing and assembly for several model species. We find that the unique error structure of ONT libraries causes errors to accumulate and assembly statistics plateau as sequence depth increases. High-quality assembled eukaryotic sequences require high-molecular-weight DNA extractions that increase sequence read length, and computational protocols that reduce error through pre-assembly correction and read selection. Our quantitative results will be helpful for researchers seeking guidance for de novo assembly projects.
Comparative severity analysis of colitis in C57BL/6 than BALB/c mice: A novel and rapid model of DSS induced colitis

Colitis is a complex and multifactorial disease with unknown etiology. To understand colitis, a number of models were developed in mouse. Colitis, in these models, was induced using either chemicals or select bacteria. Dextran sulfate sodium (DSS) induced colitis model was used widely, over other models, because of the simpler properties of DSS and similarities of the model with colitis in humans. The available models of DSS induced colitis require either longer time to understand the chronic stages of the disease or a shorter time period to study the acute phase. Currently, no composite models exist that can be used to study the acute, chronic and recovery stages of colitis within a reasonably shorter period of time. In the current study, we have developed a newer model system in two differently immune biased (Th-1 and Th-2) mice strains using DSS. We have developed the DSS model to compare the response in C57BL/6 (Th1 biased) and BALB/c (Th2 biased) mice models. We have standardized the dosage for both C57BL/6 and BALB/c mice with zero mortality rates. Using the model developed we studied the acute, chronic and recovery phases of colitis. The differential responses of C57BL/6 and BALB/c revealed that the disease was more severe in C57Bl/6. BALB/c, on the contrary, recovered from the diseased condition more quickly. The current report will further help to unravel the disease etiology based on immunological background of the host.
Nutrient Source and Mycorrhizal Association jointly alters Soil Microbial Communities that shape Plant-Rhizosphere-Soil Carbon-Nutrient Flows

Interactions between plants and microorganisms strongly affect ecosystem functioning as processes of plant productivity, litter decomposition and nutrient cycling are controlled by both organisms. Though two-sided interactions between plants and microorganisms and between microorganisms and litter decomposition are areas of major scientific research, our understanding of the three-sided interactions of plant-derived carbon flow into the soil microbial community and their follow-on effects on ecosystem processes like litter decomposition and plant nutrient uptake remains limited. Therefore, we performed a greenhouse experiment with two plant communities differing in their ability to associate with arbuscular mycorrhizal fungi (AMF). By applying a 13CO2 pulse label to the plant communities and adding various 15N labelled substrate types to ingrowth cores, we simultaneously traced the flow of plant-derived carbon into soil microbial communities and the return of mineralized nitrogen back to the plant communities. We observed that net 13C assimilation by the rhizosphere microbial communities and their community composition not only depended on plant-AMF association but also type of substrate being decomposed. AMF-association resulted in lower net 13C investment into the decomposer community than absence of the association for similar 15N uptake. This effect was driven by a reduced carbon flow to fungal and bacterial saprotrophs and a simultaneous increase of carbon flow to AMF. Additionally, in presence of AMF association CN flux also depended on the type of substrate being decomposed. Lower net 13C assimilation was observed for decomposition of plant-derived and microorganism-derived substrates whereas opposite was true for inorganic nitrogen. Interestingly, the decomposer communities assembled in the rhizosphere were structured by both the plant community and substrate amendments which suggests existence of functional overlap between the two soil contexts. Moreover, we present preliminary evidence that AMF association helps plants access nutrients that are locked in bacterial and plant necromass at a lower carbon cost. Therefore, we conclude that a better understanding of ecosystem processes like decomposition can only be achieved when the whole plant-microorganism-litter context is investigated.
Differential Response of Digesta- and Mucosa-Associated Intestinal Microbiota to Dietary Black Soldier Fly (Hermetia illucens) Larvae Meal in Seawater Phase Atlantic Salmon (Salmo salar)

Intestinal digesta is commonly used for studying responses of microbiota to dietary shifts, yet evidence is accumulating that it represents an incomplete view of the intestinal microbiota. In a 16-week seawater feeding trial, Atlantic salmon (Salmo salar) were fed either a commercially-relevant reference diet or an insect meal diet containing 15% black soldier fly (Hermetia illucens) larvae meal. The digesta- and mucosa-associated distal intestinal microbiota were profiled by 16S rRNA gene sequencing. Regardless of diet, we observed substantial differences between digesta- and mucosa-associated intestinal microbiota. Microbial richness and diversity were much higher in the digesta than the mucosa. The insect meal diet altered the distal intestinal microbiota resulting in higher microbial richness and diversity. The diet effect, however, depended on the sample origin. Digesta-associated intestinal microbiota showed more pronounced changes than the mucosa-associated microbiota. Lastly, multivariate association analyses identified two mucosa-enriched taxa, Brevinema andersonii and unclassified Spirochaetaceae, associated with the expression of genes related to immune responses and barrier function in the distal intestine, respectively. Overall, our data clearly indicate that responses in digesta- and mucosa-associated microbiota to dietary inclusion of insect meal differ, with the latter being more resilient to dietary changes.
Host and environmental determinants of microbial community structure in the marine phyllosphere

Although seagrasses are economically and ecologically critical species, little is known about their blade surface microbial communities and how these communities relate to the plant host. To determine microbial community composition and diversity on seagrass blade surfaces and in the surrounding seawater,16S rRNA gene sequencing (iTag) was used for samples collected at five sites along a gradient of freshwater input in the northern Gulf of Mexico on three separate sampling dates. Additionally, seagrass surveys were performed and environmental parameters were measured to characterize host characteristics and the abiotic conditions at each site. Results showed that Thalassia testudinum (turtle grass) blades hosted unique microbial communities that were distinct in composition and diversity from the water column. Additionally, results suggested that environmental conditions, including water depth, salinity, and temperature, were the major driver of community structure as blade surface microbial communities varied among sites and over sampling dates. Host condition may be a secondary driver of community structure as compositional changes were also correlated with host characteristics, including leaf growth rates and blade nutrient composition, Additionally, 21 microorganisms from five phyla (Cyanobacteria, Proteobacteria, Planctomycetes, Chloroflexi, and Bacteroidetes) were present in all blade surface samples and may represent a core community for T. testudinum. Members of this core community may have ecological importance for determining community structure or in performing key community functions. This study provides new insights and understanding of the processes that influence the structure of marine phyllosphere communities, how these microbial communities relate to their host, and their role as a part of the seagrass holobiont, which is an important contribution given the current decline of seagrass coverage worldwide.
Growth of Grey Kangaroos and the Reliability of Age Determination from Body Measurements II.* The Western Grey Kangaroos, Macropus fuliginosus fuliginosus, M. f. melanops and M. f. ocydromus

Seven body measurements were taken at regular intervals throughout life from both male and female western grey kangaroos of known birth date. For each sex of three subspecies and for each body measurement a growth curve was fitted, and confidence intervals calculated for determining the age of new animals. As with eastern grey kangaroos, a phase change in the growth curve was apparent at the time when the young vacate the pouch. Join points in the curve for each subspecies of western grey kangaroos were estimated empirically, as three-quarters through the interval between first emergence and final vacation of the pouch by a young animal. The growth curves were represented by a four-parameter non-linear model consisting of two hyperbolas constrained to pass through the common point. Tables presented contrast the ages at which percentile growth values are attained for each subspecies, and also provide examples of the determination of age from body measurements for both males and females, at monthly intervals during their first year. As found for the eastern grey kangaroo, head length proved to be the most reliable criterion, and all measurements of animals older than 2 years were unreliable for age determination.
Variation of water relations parameters with extended rehydration time, leaf form, season, and proportion of leaf

Pressure–volume curves were measured in October, February, and July for twigs of three deciduous, three evergreen broadleaf, four pine, and two other conifer species in the southern Appalachian Mountains, U.S.A. Data were analyzed to determine the influence on water relations parameters of rehydration time, sample leafiness, leaf form, season, and species within leaf form. Results of samples rehydrated overnight did not differ significantly from results of samples rehydrated overnight plus 24 h. Leafiness (leaf dry mass/sample dry mass) was occasionally related to water relations parameters. Water relations parameters usually varied with leaf form, and occasionally with sampling location. Patterns of variation among leaf forms differed for each combination of parameter and season: the strongest generality was that leafy deciduous twigs and pines had high tissue elasticity, whereas evergreen broadleaf species had low elasticity. Evergreen broadleaf species had a consistently high relative water content at .
Pedagogy in Health Promotion: The Scholarship of Teaching and Learning Paper of the Year Award

The purpose of this article is to provide guidance to university faculty and librarians in developing LibGuides as effective pedagogical tools in teaching/learning in undergraduateand graduate-level health promotion classes. This article presents the steps for developing and using LibGuides in course instruction as well as the evidence for their effectiveness.
An unexpected lack of difference in superoxide/H2O2 production rates in isolated heart and skeletal muscle mitochondria from a mouse model of Barth Syndrome

Barth Syndrome (BTHS) is a rare X-linked genetic disorder caused by mutations in tafazzin and characterized by loss of cardiolipin and severe cardiomyopathy. Mitochondrial superoxide/H2O2 production has been implicated in the cardiomyopathy observed in different BTHS models. There are at least 11 mitochondrial sites that produce superoxide/H2O2 at significant rates. Which of these sites generate oxidants at excessive rates in BTHS is unknown. Here, we measured the maximum capacity of superoxide/H2O2 production from each site in mitochondria isolated from heart and skeletal muscle of the tafazzin knockdown mice (tazkd) at 3, 7 and 12 months of age. Strikingly, the superoxide/H2O2 production capacities of these sites were overall indistinguishable between tazkd mice and their wildtype littermates across the time points analyzed. The only exception was site GQ in glycerol phosphate dehydrogenase, which was increased in the skeletal muscle of 7 months old tazkd mice. Mitochondrial superoxide/H2O2 production was also measured ex vivo during the oxidation of a complex mixture of substrates mimicking either heart or skeletal muscle cytosol and was found to be indistinguishable between wildtype and tazkd mice. However, we consistently measured decreased FAD-linked respiration in mitochondria isolated from tazkd mice. We conclude that the maximum capacity and ex vivo rates of superoxide/H2O2 production were not increased in mitochondria isolated from heart and skeletal muscle of tazkd mice, despite reduced oxidative capacity. Therefore, it seems unlikely that mitochondrial oxidants contribute to the development of cardiomyopathy in tazkd mice. These observations raise questions about the involvement of mitochondrial oxidants in BTHS pathology.
Toward Modeling of a General Mechanism of MPF Formation during Oocyte Maturation in Vertebrates

Abstract Vertebrate oocytes arrested at meiotic prophase I are still immature even when they reach their fully grown stage. For the acquisition of fertilizability, the fully grown oocytes must undergo oocyte maturation, during which the meiosis is released from prophase I arrest and stops again at metaphase II until inseminated. The resumption of meiosis from prophase I to metaphase II is induced by the action of maturation-promoting factor (MPF). The molecular structure of MPF is common to all eukaryotes, but the mechanisms of its formation and activation vary in cell types and in species. In this review, I summarize the mechanisms of MPF formation during oocyte maturation in two amphibian species, Xenopus laevis and Rana japonica. In Xenopus, immature oocytes are equipped with inactive MPF (pre-MPF) sufficient for completing oocyte maturation, and therefore only its activation is required after hormonal stimulation. In contrast, immature Rana oocytes contain no pre-MPF. Therefore, MPF must be newly formed during oocyte maturation, as is the case in fishes and other amphibians (toads and newts). The mechanism of MPF formation in Xenopus therefore seems to be different to that in other lower vertebrates. However, I wish to propose a new mechanism of MPF formation that might be appropriate for all species of lower vertebrates, inclusive of Xenopus, based on the novel concept that pre-MPF is an artifact produced under unnatural conditions and is not an essential molecule for initiating oocyte maturation, in contradiction to the generally believed notion that pre-MPF is actively stocked for the initiation of oocyte maturation. The standpoint that pre-MPF is not indispensable for initiating oocyte maturation might provide a new insight into the mechanism of MPF formation during oocyte maturation, allowing us to model a comprehensive mechanism applicable to all vertebrates, including mammals.
The Tumor Microenvironment: A Milieu Hindering and Obstructing Antitumor Immune Responses

The success of cancer immunotherapy relies on the knowledge of the tumor microenvironment and the immune evasion mechanisms in which the tumor, stroma, and infiltrating immune cells function in a complex network. The potential barriers that profoundly challenge the overall clinical outcome of promising therapies need to be fully identified and counteracted. Although cancer immunotherapy has increasingly been applied, we are far from understanding how to utilize different strategies in the best way and how to combine therapeutic options to optimize clinical benefit. This review intends to give a contemporary and detailed overview of the different roles of immune cells, exosomes, and molecules acting in the tumor microenvironment and how they relate to immune activation and escape. Further, current and novel immunotherapeutic options will be discussed.
An artificial diet for aphidophagous syrphids, Episyrphus balteatus (de Geer) and Eupeodes bucculatus (Rondani) (Diptera: Syrphidae) using drone honeybee brood powder

We reared two aphidophagous syrphid species, Episyrphus balteatus and Eupeodes bucculatus, on artificial diets throughout all larval stages but their development was inferior to those feeding on natural prey (aphids). Drone honeybee brood powder (DP) offered the minimum nutrition necessary for larval development in both species. E. balteatus grew to adulthood on the original DP diet, but E. bucculatus did not. An agar-gel diet containing DP improved the survival rate of E. bucculatus and half the larvae on this diet reached adulthood. Diet softness was a very important physical factor for rearing syrphid larvae. The amount of food consumed by third-instar larvae of E. bucculatus was measured. The results showed sufficient intake of DP by the larvae. The addition of autolyzed yeast and sucrose to the diet improved larval development.
What Is Youth Political Participation? Literature Review on Youth Political Participation and Political Attitudes

Looking at political participation behavior of young adults in contemporary Europe, this paper provides the reader with a map of different terminologies and logics that are used to discuss youth political participation. The existing literature is examined through the lens of five guiding questions: what defines youth political participation? How does youth political participation differ from adult political participation? How do young adults develop political attitudes? How does youth political participation differ across Europe? What methods are being used to analyze youth political participation? For those researching youth political participation for the first time, this paper offers a useful overview of the topic. At the same time, it gives researchers who are already well-informed the opportunity to reflect on the current state of research in this field. Finally, this paper indicates where future research is needed.
Gut Microbiota and Gestational Diabetes Mellitus: A Review of Host-Gut Microbiota Interactions and Their Therapeutic Potential

Gestational diabetes mellitus (GDM) is defined as impaired glucose tolerance recognized during pregnancy. GDM is associated with metabolic disorder phenotypes, such as obesity, low-grade inflammation, and insulin resistance. Following delivery, nearly half of the women with a history of GDM have persistent postpartum glucose intolerance and an increased risk of developing type 2 diabetes mellitus (T2DM), as much as 7-fold. The alarming upward trend may worsen the socioeconomic burden worldwide. Accumulating evidence strongly associates gut microbiota dysbiosis in women with GDM, similar to the T2DM profile. Several metagenomics studies have shown gut microbiota, such as Ruminococcaceae, Parabacteroides distasonis, and Prevotella, were enriched in women with GDM. These microbiota populations are associated with metabolic pathways for carbohydrate metabolism and insulin signaling, suggesting a potential “gut microbiota signature” in women with GDM. Furthermore, elevated expression of serum zonulin, a marker of gut epithelial permeability, during early pregnancy in women with GDM indicates a possible link between gut microbiota and GDM. Nevertheless, few studies have revealed discrepant results, and the interplay between gut microbiota dysbiosis and host metabolism in women with GDM is yet to be elucidated. Lifestyle modification and pharmacological treatment with metformin showed evidence of modulation of gut microbiota and proved to be beneficial to maintain glucose homeostasis in T2DM. Nonetheless, post-GDM women have poor compliance toward lifestyle modification after delivery, and metformin treatment remains controversial as a T2DM preventive strategy. We hypothesized modulation of the composition of gut microbiota with probiotics supplementation may reverse postpartum glucose intolerance in post-GDM women. In this review, we addressed gut microbiota dysbiosis and the possible mechanistic links between the host and gut microbiota in women with GDM. Furthermore, this review highlights the potential therapeutic use of probiotics in post-GDM women as a T2DM preventive strategy.
A metabolic CRISPR-Cas9 screen in Chinese hamster ovary cells identifies glutamine-sensitive genes

Over the past decades, optimization of media formulation and feeding strategies have fueled a many-fold improvement in CHO-based biopharmaceutical production. While Design of Experiments (DOE) and media screens have led to many advances, genome editing offers another avenue for enhancing cell metabolism and bioproduction. However the complexity of metabolism, involving thousands of genes, makes it unclear which engineering strategies will result in desired traits. Here we developed a comprehensive pooled CRISPR screen for CHO cell metabolism, including ~16,000 gRNAs against ~2500 metabolic enzymes and regulators. We demonstrated the value of this screen by identifying a glutamine response network in CHO cells. Glutamine is particularly important since it is often substantially over-fed to drive increased TCA cycle flux but can lead to accumulation of toxic ammonia. Within the glutamine-response network, the deletion of a novel and poorly characterized lipase, Abhd11, was found to substantially increase growth in glutamine-free media by altering the regulation of the TCA cycle. Thus, the screen provides an invaluable targeted platform to comprehensively study genes involved in any metabolic trait.
A new species of Jainus (Monogenea), gill parasite of Schizodon borellii (Characiformes, Anostomidae) from the upper Paraná river floodplain, Brazil

Jainus piava n. sp. is described from the gills of Schizodon borellii (Boulenger, 1900) (Characiform), commonly named as piava from the upper Parana River floodplain, Brazil. The new species differs from the other members of Jainus in the following features: ventral bar thin broadly V-shaped and male copulatory organ (MCO) a coil of about 1.5 rings. Jainus piava n. sp. is similar to species of Jainus by having a ventral anchor base with flattened superficial root and elongate rodlike deep root.