Miracle-dz/UniFAR-FTUs huggingface dataset:
Heterochrony in brontothere horn evolution: allometric interpretations and the effect of life history scaling

The Brontotheriidae (Perissodactyla, Mammalia) are often used as an illustration of vertebrate macroevolutionary trends because their morphological evolution includes significant size increases accompanied by the disproportionate lengthening of bony frontonasal horns. The positive phylogenetic allometry for horn length vs. skull length is among the strongest known of such relationships in vertebrate phylogeny. Hypotheses explaining the change from small, incipient horns in Eocene ancestors to longer horns in Oligocene descendants have included two heterochronic mechanisms, hypermorphosis (extrapolation) and predisplacement (earlier onset time of horn growth). These proposed peramorphic mechanisms derive from interpretation of adult intergeneric allometries in logarithmic data spaces. Analysis of the raw (unlogged) data shows that the simple allometric model previously used is not an appropriate model for this specific problem. The heterochronic interpretations derived from them are therefore unsupported (but not disproven) by the allometries. A more appropriate allometric model for the data (full model) does not support any heterochronic interpretation. Previously unaccounted for in the heterochronic hypotheses is a complication due to body-size scaling effects on life history stage lengths. Neontological scaling patterns suggest that brontothere size increases were probably accompanied by increasing life spans and longer developmental stages. This effect broadens the types of heterochronies that may be postulated. Semiquantitative analyses comparing brontotheres with similarly sized extant ungulates show the hypothesized effect of larger size on brontothere life history stages. A scaled descendant ontogeny introduces the problem of relative vs. absolute time frames within which to view ontogenetic onset times. Thus, predisplacements, postdisplacements, or nondisplacements may be viewed as relative or absolute with respect to ancestral ontogenies. This raises a fundamental question about how development scales, which in turn affects how heterochronies are interpreted. A scaling effect suggests that brontothere horns are more likely postdisplaced in the traditional absolute time sense. Paradoxically then, while the descendant adult horn is peramorphic, its onset time may have shifted in a paedomorphic direction. Data for two Oligocene juvenile brontotheres suggest that most horn growth occurred late in their longer (i.e., descendant) ontogenies (hypermorphosis), and that the horns probably grew at faster rates (acceleration) than in Eocene taxa.
Animal models as indicators of immunogenicity of therapeutic proteins in humans.

: Animal models have not been able to predict the immunogenicity of therapeutic proteins in humans reliably. The main issue is that administration of a human protein in an animal species is likely to be immunogenic. In non-human primate studies, we have seen a variety of responses; from little to no antibody response, to a strong neutralizing response, or even a cross-reactive antibody response. These have generally not correlated well with the immune response seen in humans. The route of administration, duration and schedule of dosing, the cumulative dosage of the protein, the pharmacological (i.e., immune altering) properties of the protein, as well as the purity of the clinical material can influence the immunogenicity. The animal studies should mimic these factors to the best extent possible for the animal model to be at all relevant to humans. Models do exist which provide valuable information to compare the immunogenicity of various compounds or routes of administration. Presumably, this 'relative' immunogenicity would be similar in humans. Additional characterization of transgenic mice, or use of homologous proteins, may help to establish better models to predict immunogenicity.
Gut Microbiome Derived Metabolites to Regulate Energy Homeostasis: HowMicrobiome Talks to Host

Gut microbiome recently known to be one the major player in regulating several physiological functions in normal and pathological conditions of human diseases [1]. There is always a curios question remains to non-expert in the field that how gut microbiome interacts with host cells and impacts cellular metabolism. For experts, unraveling these facts and discussing them, always brings new viewpoints in the field to further study that can be critical to uncover new drug targets and biomarkers of metabolic diseases. The prevalence of two metabolic diseases i.e., obesity and type 2 diabetes are on peak, and are associated with several life threatening consequences like cardiovascular diseases, brain disorders and cancer [2]. Gut microbiome contributes significantly in the pathology of obesity and diabetes [3,4]. As initial studies showed that transplantation of obese gut microbiome to distinct recipient have ability to transfer obesity from donor to recipient in mice, suggesting gut microbiome carries certain intrinsic factors that interacts with host metabolism and develops metabolic derangements. Several pathways have been proposed to be modulated by gut microbiome to cause metabolic syndrome, some of them are as follows; 1) gut microbiome helps to harvest extra energy from food that further increase extra energy accumulation in fat tissues, 2) gut microbiome mediated endotoxemia to create low grade inflammation and 3) production of certain detrimental metabolites that implicates dysregulation of several cellular function to aggravate disease progression [3,5]. For example, gut microbiome-derived TMAO induces cardiovascular diseases, acetate impairs insulin secretion and LPS escalates obesity and type 2 diabetes via increasing low grade inflammation [5-7]. To answer the question how microbiome interacts with host cells and impact metabolic function, later point explains the better link between gut microbiome and host in normal physiology.
Comparison of Expression Profiles of HOX Gene Family in Human Embryonic Stem Cells and Selected Human Fetal Tissues

The HOX genes coding homeodomain proteins have been suggested as a candidate molecular switch that determines the fates of cells during embryonic development and patterning. It is believed that a set of differentiation-specific HOX genes enter into a turn-on state during tissue differentiation, in contrast to stem cell-specific HOX genes that enter into a turn-off state. However, comprehensive data of expression profiles of HOX genes in human embryonic stem cells (hESC) and differentiated embryonic tissues are not available. In this study, we investigated the expression patterns of all 39 HOX genes in hESC and human fetal tissues and analyzed the relationships between hESC and each tissue. Of the 39 genes, 18 HOX genes were expressed in stem cells, and diverse expression patterning was observed in human fetal tissues when compared with stem cells. These results indicate that HOX genes could be main targets for switching of stem cell differentiation into tissues.
Effects of a Specific Nutrient on Feed Intake, Digestion and Rumen Counts of Anaerobic Fungi and Bacteria

Reliance on seasonally poor quality pasture is a feature of the grazing industries in many areas of Australia. Ruminant production is often restricted by the inefficient digestion of feeds that contain high levels of fibre. The slow rate of fiber degradation in the rumen reduces the flow of digesta through the gut and limits feed intake. Anaerobic fungi are one of the fibre digesting populations in the rumen (Gordon and Phillips, 1998) and studies with sheep have indicated that they make a large contribution in digestion of fibrous diets (Gordon and Phillips, 1993). Akin et al. (1983) found that fungal populations and activity were greatly diminished in diets low in sulphur. It has been suggested that the low sulphur content of many poor quality pastures could result in reduced fungal numbers and limited fibre digestion (Gordon and Phillips, 1998). In this study we have tested the ability of a sulphur supplement, mercaptopropanoic acid (MPA), to boost the number of fungi and improve digestion in sheep fed a poor quality straw diet. MPA is slowly degraded in rumen digesta in vitro and is utilized by a variety of anaerobic fungi (Phillips and Gordon, unpublished). The study was conducted with 13 cross bred wethers kept in metabolism cages and fed, ad libitum, a diet of alkali-treated wheat straw supplemented with urea and minerals (Weston et al., 1988). The study was in three periods: (1) adjustment to the diet for 14 days; (2) seven sheep were supplemented with MPA for 21 days and six were unsupplemented; (3) the treatments in period 2 were alternated. Comparisons were made for each animal between the unsupplemented and the supplemented periods. The MPA was infused directly into the rumen via a permanent cannula at the rate of 0.6 g/d (0.19 g S/d). Collections of feed refusals and faeces for the calculation of voluntary feed intake and whole tract digestibilities were done for the last 14 days of the treatment periods. Samples of rumen digesta were collected on the final day of each treatment period and the numbers of fungal zoospores and total bacteria were assessed by culture using roll tubes (Gordon and Phillips, 1993). When sheep were receiving MPA, the fungal count was 15 times higher (+ log10 1.2) than during the control period (Table). In contrast bacterial numbers were similar in both periods suggesting that MPA was selectively boosting fungal numbers rather than contributing to the overall sulphur pool of the rumen. In this study, as previously (Akin et al., 1983; Gordon and Phillips, 1993), a large increase in fungal numbers was associated with a substantial increase in feed intake (+25%, Table 1). There were also improvements in digestibility leading to a large increase in dry matter digestion (+37%). These results suggest that MPA supplementation may be a means of boosting fungal numbers and thus increasing the feed intake of sheep grazing poor quality pasture. Support for this project was provided by Australian woolgrowers and the Australian Government through the Australian Wool Research and Promotion Organisation.
Functional Morphology of the Feeding Apparatus in Simenchelys parasitica (Simenchelyinae: Synaphobranchidae), an Alleged Parasitic Eel

The Pugnose Eel, Simenchelys parasitica (family Synaphobranchidae, subfamily Simenchelyinae), is a deep-water species described as both being a parasite and a scavenger that can bite off large chunks of flesh. Little, however, is known about its cranial morphology, including to what degree its feeding apparatus is modified to allow feeding specializations. We provide a detailed description of the cranial morphology of S. parasitica, comparing it with that of more closely related synaphobranchid species, for which no parasitic behavior has been reported, i.e., Ilyophis brunneus (Ilyophinae) and Synaphobranchus brevidorsalis (Synaphobranchinae). Pugnose Eels have stretchable skin around a small, terminal mouth, as well as teeth with a clear cutting edge, a mouth-closing apparatus equipped with large jaw muscles, a large tongue-like secretory structure, and well-developed hyoid and branchial arches to facilitate the transport of large food items in the buccal cavity. A comparison with other species provides several lines of evidence supporting the hypothesis that Pugnose Eels have a feeding apparatus that is equipped for biting off chunks of flesh from prey (irrespective of whether prey is dead or alive), most likely by using rotational feeding.
Clustering of QTL conferring SCMV resistance in maize

Sugarcane mosaic virus (SCMV) is an important virus disease of maize (Zea mays L.) in Europe. In this study, we mapped and characterized two major quantitative trait locus (QTL) regions conferring resistance to SCMV in a maize population consisting of 121 F 3 lines from cross F7 (susceptible) x FAP1360 (resistant). This population was evaluated for SCMV resistance in replicated field trials across two environments under artificial inoculation. Two previously identified chromosome regions (chromosome 6S and 3L) containing QTL conferring resistance were mapped with 24 SSR markers by composite interval mapping. Both regions together explained between 33.0% and 71.1% of the phenotypic variance for SCMV resistance according to the stage of plant development. The Scmv1 region harbored two QTL rather than one QTL as identified in previous studies. Clustering of QTL for SCMV resistance was confirmed for at least one chromosome region.
Role of fibroblast growth factor receptor in regulation of membrane traffic

Several studies show that membrane transport mechanisms are regulated by signalling molecules. Recently, genome-wide screen analyses in C.elegans have enabled scientists to identify novel regulators in membrane trafficking and also signalling molecules which are found to couple with this machinery. Fibroblast growth factor (FGF) via binding to fibroblast growth factor receptor (FGFR) mediate signals which are essential in the development of an organism, patterning, cell migration and tissue homeostasis. Impaired FGFR-mediated signalling has been associated with various developmental, neoplastic, metabolic and neurological diseases and cancer. In this study, the potential role of FGFR-mediated signalling pathway as a regulator of membrane trafficking was investigated. The GFP-tagged yolk protein YP170-GFP trafficking was analysed in worms where 1) FGFR signalling cascade components were depleted by RNAi and 2) in mutant animals. From these results, it was found that the disruption of the genes egl-15 (FGFR), egl-17(FGF), let-756(FGF), sem-5, let-60, lin-45, mek-2, mpk-1 and plc-3 lead to abnormal localization of YP170-GFP, suggesting that signalling downstream of FGFR via activation of MAPK and PLC-γ pathway is regulating membrane transport. The route of trafficking was further investigated, to pinpoint which membrane step is regulated by worm FGFR, by analysing a number of GFP-tagged intracellular membrane markers in the intestine of Wild Type (WT) and FGFR mutant worms. FGFR mutant worms showed a significant difference in the localisation of several endosomal membrane markers, suggesting its regulatory role in early and recycling steps of endocytosis. Finally, the trafficking of transferrin in a mammalian NIH/3T3 cell line was investigated to identify the conservation of these membrane trafficking regulatory mechanisms between organisms. Results showed no significant changes in transferrin trafficking upon FGFR stimulation or inhibition.
Seed Germination Ecology of Catchweed Bedstraw (Galium aparine)

The influence of temperature, light, solution pH, water stress, salt stress, and burial depth on seed germination and seedling emergence of catchweed bedstraw and the sensitivity of that weed to commonly available herbicides in China were studied in laboratory and greenhouse. Germination occurred at day/night temperatures from 5/0 C to 30/25 C, with optimum germination at 15/10 C. Catchweed bedstraw germinated equally well under a 12-h photoperiod and continuous darkness; however, a 24-h photoperiod inhibited seed germination. Catchweed bedstraw seed is moderately sensitive to osmotic potential and salt stress, with 15 and 3% germination rates at an osmotic potential of −0.5 Mpa and salinity level of 120 mM, respectively. Maximum seed germination was observed in near neutral pH; germination was greater than 80% over a broad pH range from 5 to 8. Seedling emergence of the seeds buried at a depth of 1 cm was higher (74%) than those placed on the soil surface (20%), but declined with burial depth increasing. Few (10%) seedlings emerged when seeds were placed at a depth of 5 cm. Bensulfuron-methyl, and ethametsulfuron-methyl applied PRE and tribenuron-methyl, fluroxypyr, and florasulam applied POST can be used to provide greater than 80% control of catchweed bedstraw. The results of this study have contributed to more complete understanding of the germination and emergence of catchweed bedstraw. Nomenclature: Catchweed bedstraw, Galium aparine L.
Evidence of local adaptation to fine‐ and coarse‐grained environmental variability in Poa alpina in the Swiss Alps

In the alpine landscape, characterized by high spatiotemporal heterogeneity and barriers, divergent selection is likely to lead to local adaptation of plant populations either through adaptive genetic differentiation or through phenotypic plasticity. The relative importance of these processes has rarely been investigated in relation to the spatial scale of environmental heterogeneity. In this study, we used reciprocal transplantation experiments of populations across nearby and distant field sites to shed light on these complementary processes. We reciprocally transplanted populations of the widespread alpine grass, Poa alpina, within and across regions in the Swiss Alps. We inferred local adaptation at the metapopulation level by comparing fitness of plants transplanted to their site of origin and to nearby or distant novel sites. Additionally, we measured specific leaf area (SLA) and performed selection analyses to investigate directional selection on mean trait value at each field site and on the degree of plasticity of this trait to assess whether plastic responses were adaptive. In parallel, all populations were genotyped with microsatellite markers to assess neutral molecular differentiation. Molecular differentiation was high among populations within and among regions, indicating restricted gene flow among P. alpina populations. Reproductive biomass was highest in individuals grown in their region of origin, revealing local adaptation to coarse‐grained environmental variability. Similarly, inflorescence height, associated with reproductive biomass, reflected adaptation to fine‐ and coarse‐grained environmental variability. Furthermore, we found evidence that plasticity in SLA across coarse‐grained habitats was correlated with plant fitness, suggesting that plasticity in this trait is adaptive. Synthesis. Our results revealed adaptive genetic differentiation between P. alpina populations in the Swiss Alps reflecting local adaptation. Furthermore, high phenotypic plasticity in SLA contributed to the maintenance of fitness homoeostasis across habitats. Hence, adaptive genetic differentiation and phenotypic plasticity play a complementary role for adaption of P. alpina to environmental heterogeneity in the Swiss Alps and both may be critical to mitigate local extinction risk under rapid climate change.
In vitro gas and methane production of two mixed rations influenced by three different cultures of Saccharomyces cerevisiae

ABSTRACT The current study aimed to evaluate if the effect of Saccharomyces cerevisiae (SC) on in vitro fermentation can be affected with the crude protein (CP) content of the ration. Three commercial SC cultures of Biocell F53®, Procreatin 7®, and Biosaf SC47® were evaluated at 0 (SC0), 2 (SC2), and 4 (SC4) mg/g dry matter (DM) of substrate. Two rations with 13% (low crude protein [LCP]) and 16% CP (high crude protein [HCP]) were used as substrates. Rumen gas (gas production [GP]) and methane (CH4) productions were recorded. The HCP ration had increased (P = .05) asymptotic GP, CH4 production, and fermentation parameters. Biocell F53® and Biosaf SC47® increased the asymptotic GP (P < .05) in HCP and LCP rations with better effect for the dose of 2 mg/g DM substrate HCP (P < .05) and dose of 4 mg yeast/g DM substrate with the LCP ration. The highest CH4 production was observed (P < .05) with Procreatin 7®. It could be concluded that HCP ration improved GP than LCP ration. Moreover, addition of Biocell F53® and Biosaf SC47® at rate of 2 mg/g DM improved fermentation kinetics and nutrients degradability. Abbreviations:b: the asymptotic gas production; c: the rate of gas production; CH4: methane; GY24: gas yield at 24 h of incubation; L: the initial delay before gas production begins; MCP: microbial CP production; PF24: partitioning factor at 24 h of incubation.
Neuropeptidomics: The Characterization of Neuropeptides and Hormones in the Nervous and Neuroendocrine Systems

Ning Yang, Samuel J. Irving, Elena V. Romanova, Jennifer W. Mitchell, Martha U. Gillette, and Jonathan V. Sweedler 1 Department of Chemistry and the Beckman Institute, University of Illinois at Urbana‐Champaign, Urbana, Illinois, USA 2 Department of Molecular and Integrative Physiology, University of Illinois at Urbana‐Champaign, Urbana, Illinois, USA 3 Department of Cell and Developmental Biology and the Beckman Institute, University of Illinois at Urbana‐Champaign, Urbana, Illinois, USA chapter 8
Biodegradable Plastic and Fabric Mulch Performance in Field and High Tunnel Cucumber Production

S UMMARY . Polyethylene mulch use is common in vegetable production, but disposal of mulch is problematic for growers and of signiﬁcant environmental concern. Biodegradable fabrics and plastic ﬁlms are compostable and can be incorporated into the soil at the end of the growing season, but questions remain about the durability, performance, and rate of decomposition of these products after soil incorporation. Three trials were conducted in ﬁeld and high tunnel cucumber ( Cucumis sativus ) cropping systems to compare performance and decomposition after use among two bioplastic ﬁlms and four experimental spunbond, nonwoven biofabrics. Soil temperature and moisture, mulch durability and deterioration, weed suppression, and crop yield data were collected in each growing season. All biomulches were soil incorporated after the growing season and recovered up to 11 months after incorporation to estimate relative rates of decomposition. One bioplastic ﬁlm increased ﬁeld soil temperature by 2 (cid:1) C in 2013, but temperatures under the biofabrics were not different from bare soil. Bioplastics and biofabrics increased soil moisture relative to bare soil. Bioplastic ﬁlms were less durable and deteriorated sooner than biofabrics, especially in the ﬁeld environment (as early as 34 days after transplanting). All biomulches suppressed weed emergence relative to bare soil, but weeds were visibly growing beneath the most translucent biofabric. Marketable yield of cucumber was trending highest in the most durable and opaque biofabric (1827 g (cid:1) m L 2 ), but was not signiﬁcantly different from weed-free bare soil (1251 g (cid:1) m L 2 ). Relative rate of mulch decomposition up to 11 months after soil incorporation was not different among bioplastic and biofabric products. Results suggest that the tested biofabrics will be most useful to growers when soil warming is not necessary (e.g., warm climates), but moisture conservation and weed control are critical (e.g., organic cropping systems). Moreover, biofabrics are permeable and may be useful to growers dependent on sprinkler irrigation or rainfall to meet crop water demands.