Miracle-dz/UniFAR-FTUs huggingface dataset:
Neoagarotetraose-modulated gut microbiota and alleviated gut inflammation in antibiotic treatment mice

ABSTRACT This study aimed to explore the effects of neoagarotetraose (NAT) on gut microbiota composition and inflammation after antibiotic treatment. Our results showed that NAT significantly increased the length of colon (P < .01) and decreased the ileocecal valve index (P < .05), and reduced IFN-γ content (P < .01) and downregulated the IFN-γ/IL-4 ratio (P < .01), suggesting that NAT mediated the balance of the Th1/Th2 ratio to maintain the immune equilibrium of the intestinal mucosa. Our data showed that NAT prohibited intestinal inflammation by increasing antimicrobial peptides and gut integrity. Furthermore, NAT administration significantly increased the fecal concentration of total short-chain fatty acids. In addition, NAT had the ability to modulate gut microbiota composition and diversity. In our study, significantly increased Bifidobacterium, Lactobacillus and Prevotella were observed in the NAT group (P < .01). In summary, all of these results demonstrated that NAT was a potential prebiotic for modulating intestinal microbiota and promoting host health.
Macrophage-to-sensory neuron crosstalk mediated by Angiotensin II type-2 receptor elicits neuropathic pain

Peripheral nerve damage initiates a complex series of cellular and structural processes that culminate in chronic neuropathic pain. Our study defines local angiotensin signaling via activation of the Angiotensin II (Ang II) type-2 receptor (AT2R) on macrophages as the critical trigger of neuropathic pain. An AT2R-selective antagonist attenuates neuropathic, but not inflammatory pain hypersensitivity in mice, and requires the cell damage-sensing ion channel transient receptor potential family-A member-1 (TRPA1). Mechanical and cold pain hypersensitivity that are characteristic of neuropathic conditions can be attenuated by chemogenetic depletion of peripheral macrophages and AT2R-null hematopoietic cell transplantation. Our findings show no AT2R expression in mouse or human sensory neurons, rather AT2R expression and activation in macrophages triggers production of reactive oxygen/nitrogen species, which trans-activate TRPA1 on sensory neurons. Our study defines the precise neuro-immune crosstalk underlying nociceptor sensitization at the site of nerve injury. This form of cell-to-cell signaling represents a critical peripheral mechanism for chronic neuropathic pain, and therefore identifies multiple analgesic targets.
Hydraulic constraints of reproduction do not explain sexual dimorphism in the genus Leucadendron (Proteaceae)

Because of the importance of reproduction in plant life history, the physiological costs of reproduction often influence vegetative structure and function. In dioecious species, these effects can be quite obvious, as different costs of male and female reproductive functions are entirely separated among different individuals in a population. In fire-prone ecosystems, in which recruitment is driven by fire frequency, many plants will maintain their seeds in the canopy, only to be released after a fire. The dioecious genus Leucadendron is a notable case of this, as females can maintain their seed cones for years, and, even more interestingly, species in the genus differ substantially in the degree to which males and females are sexually dimorphic. A recent study (Harris and Pannell 2010) argued that the hydraulic costs of maintaining seed cones for many years would effect the degree of sexual dimorphism among species. However, this assumed that shoot hydraulic architecture would be related to traits exhibiting sexual dimorphism. Here we explicitly test this hypothesis on two Leucadendron species. We found (1) that metrics of branch ramification used in the previous study to characterize dimorphism do not conform to known scaling relationships and (2) that sexual dimorphism in shoot architecture has no effect on hydraulic efficiency. Both of these results seriously question the pattern described by Harris and Pannell (2010) and suggest that the hydraulic costs of prolonged seed retention in Leucadendron do not significantly affect branch architecture.
Broadcast Baits for Fire Ant Control

Disclaimers The products listed have been found to reduce the number of fire ant colonies compared to those in untreated plots in replicated scientific tests conducted by the Texas Agricultural Extension Service. Because of rapid changes in product development, regulatory and market conditions and ongoing scientific research, the information given and product availability may change; they are the most accurate available at the time of printing. The lists are not intended to be comprehensive. Product brand names are used as a service to the reader. Neither the Extension service nor the Texas Fire Ant Research and Management Plan endorses or discourages the use of any of the products mentioned.
Growth, survival, carbon rates for some dry tropical forest trees used in enrichment planting in the Cerro Blanco protected forest on the Ecuadorian coast

ABSTRACT Deforestation principally to establish cattle pastures has created large expanses of land dominated by exotic grass prior to the establishment of the Cerro Blanco Protected Forest in Ecuador. A dry forest restoration program was carried out from 2008 to 2017. Tree planting sites were cleared in parallel lines through abandoned pasture and secondary vegetation using manual labor. Native tree species were produced in a nursery on site and used in yearly plantings during the rainy season. A total of 637 hectares were planted at an average stocking density of 1,000 trees per hectare. Growth data was collected from trees planted in nine sites from 2008 to 2017. Mortality rates were determined from a sample of 400 trees of twenty-two species. Survival of all species was greater than 50%. Ten species had survival rates greater than 90%. Vitex gigantea, with high survival rates, also had significantly greater growth rates than the other species (p < 0.0001) and showed the greatest yearly accumulation of total carbon (2.07 Kg C yr −1 stem−1). Other species with high growth rates were Cordia alliodora and Centrolobium ochroxylum. This restoration program demonstrates that the dry forest restoration with timely maintenance and protection from fire and grazing is possible with intensive tree planting of native species.
An environmental metabolomics study of the effect of abiotic substances on Pseudomonas putida by employing analytical techniques

16 Declaration . 17 Copyrights Statement . 18 Dedication . 19 Acknowledgment . 20 Abbreviations and Acronyms . 21 Preface . 24 1 Chapter 1: Literature review . 25 1.
Defective Immune Regulation in Multiple Sclerosis: E3 Ubiquitin Ligase Cbl-b and TLR Tolerance

Multiple sclerosis (MS) is an autoimmune disease of the central nervous system (CNS) with unknown etiology. The variable response to therapy in MS suggests a need for personalized approaches based on genetic differences. Genome-wide association studies have linked CBLB genetic variants with MS. Cbl-b is an E3 ubiquitin ligase that regulates T cell activation and Cbl-b-deficient () mice show T cell abnormalities described in MS patients. Our observation of an aberrant trafficking of Cbl-b T cells led us to ask whether the MS drug, FTY720, postulated to modulate T cell trafficking, is less effective in Cbl-b mice during EAE. We documented that FTY720 significantly inhibits EAE in Cbl-b mice, suggesting that MS patients with potential Cbl-b abnormalities may still be excellent candidates for FTY720 treatment. In addition to the autoimmune phenotype, Cbl-b mice demonstrate enhanced anti-tumor immunity. Cbl-b T cells are resistant to multiple immunoregulatory mechanisms such as Tregs. PD-L1/PD-1 is an important immunoregulatory pathway and a target in cancer immunotherapy. We have now discovered that Cbl-b T cells and NK cells are resistant to PD-L1/PD-1. These results suggest that targeting Cbl-b in cancer immunotherapy provides an approach to simultaneously override numerous immunoregulatory checkpoints.
Reviewing the impacts of coffee certification programmes on smallholder livelihoods

ABSTRACT Certification programmes and voluntary standards for sustainability are now a common feature of many agricultural landscapes worldwide. The rapid expansion of such programmes has only recently been accompanied by concerted attempts to assess the lived experience of enrolled producers. This article reviews empirical research assessing the impact of certification programmes on coffee smallholder livelihood assets, and presents an initial framework for both conceptualising and analysing change in livelihood assets resulting from certification. Several of the reviewed studies identified enhanced livelihood assets arising from certification under specific institutional and contextual settings, but causation was difficult to establish. A greater number of studies found either neutral or mixed impacts, and a small number reported negative impacts. While a consensus has yet to be reached regarding all livelihood impacts of certification programmes, we present a series of propositions that reflect widely reported impacts. Further findings drawn from the review include: (i) stronger pre-existing institutions within the producer community are more likely to result in benefits for individual households; (ii) the value chain structures through which certification programmes are implemented are highly varied and strongly influence livelihood outcomes; and (iii) methodologically, existing studies rarely present either reliable baseline data or a realistic control group for comparison, making causation difficult to establish. EDITED BY Dagmar Mithöfer
A comparison of Barred and Spotted Owl nest-site characteristics in the Eastern Cascade Mountains, Washington

--We describe 10 nest sites of the northern Barred Owl (Strix varia varia) in mixed-coniferous forests of the eastern Cascades in Washington, a region where the species is syrupattic with the northern Spotted Owl (S. occidentalis caurina). Our goal was to determine whether Barred and Spotted owls used similar habitats for nesting. In contrast to Spotted Owls, Barred Owl nest sites were situated on gentle slopes or fiat ground, closer to water, and included more hardwoods and a greater richness of tree species. Barred Owl nests were usually in cavities or platforms created at the broken top of the tree bole. Only two Barred Owl nests were in abandoned hawk nests or clumps of branches infected by dwarfmistletoe (Arceuthobium douglasii), which were the two most common nest structures used by Spotted Owls in our study area. Barred Owls used a greater range of tree species for nesting, including three nests in black cottonwoods (Populus trichoca,pa), a species rarely used for nesting by Spotted Owls in the Pacific Northwest. Although differences in these attributes suggest that the two species used somewhat different habitats, Barred Owls have become more abundant in our study area and the region, and further assessments of habitat use may indicate greater niche overlap.
The Neurobiological Basis of Voluntary Exercise in Selectively-Bred High Runner Mice

Author(s): Thompson, Zoe | Advisor(s): Garland, Jr., Theodore | Abstract: Exercise is a rewarding behavior with a multitude of positive effects on the body and brain, and animals vary greatly in terms of how much they choose to exercise. I examined neurobiological changes that have occurred in four replicate lines of mice selectively bred for high voluntary wheel running as compared with four non-selected control lines. First, I followed up on a study which showed that high runner (HR) mice have larger midbrains than control (C) mice. I wanted to determine which midbrain regions have increased in size, and whether 10 weeks of wheel access would affect their size and/or cell density. I found a significant interaction between linetype (HR vs. C) and wheel access in the periaqueductal grey (PAG) region, with wheel access increasing PAG volume in C mice, while decreasing it in HR mice. HR mice also tended to have a larger ventral tegmental area, a region involved in processing rewards. Next, I examined plasma levels of two endocannabinoids, 2-arachidonylglycerol (2-AG) and anandamide (AEA), in male and female HR and C mice with or without 6 days of wheel access (as used in the routine selection protocol). I found a significant interaction between sex, linetype, and wheel access, with female mice having lower levels of 2-AG and wheel access lowering 2-AG in some subgroups. The amount of running in the 30 minutes before sampling was a significant predictor of AEA levels in mice with wheel access, and HR had lower levels than C. My third chapter examined reward substitution. Mice were housed with or without wheels and given access to artificial sweeteners as competing rewards. Building on data previously collected, we showed that all mice drank more of the artificial sweetener blends compared to water, although this increase was significantly smaller in HR mice, and only when they had access to wheels. This result suggests that HR mice prefer the reward of wheel running over that from sweeteners. Overall, I show that HR mice have evolved several neurobiological differences that contribute to their ability to voluntarily exercise ~3 times as much as C mice on a daily basis.
A ciliated epithelium covering the inner surface of the glove finger in Balaenoptera physalus Linnaeus, 1758

Studied the glove finger in B. physalus, which is protruding from the buUa tympani into the external auditory meatus. Histological examination revealed that the inner surface of this structure is covered by an epithelium which is composed of ciliated cells alternating with secretory cells. The presence of this epithelium allowed some conclusions about the origin of the glove finger in Balaenopteridae.
Onset of quorum sensing and exopolysaccharide production in single cells within growing microcolonies

The aim of this experiment is to understand colony behavior and other phenomena such as quorum sensing. The latter enables bacteria to restrict the expression of specific genes to the high cell densities at which the resulting phenotypes will be most beneficial. In these datasets, mVenus (yellow) is driven by cell division, meaning that any cell which is yellow has either recently undergone cell division, or is about to, or both. mCherry (red) represents QS signal production. This is the most heterogeneous channel. Cerulean (blue) represents exopolysaccharide production, which can only occur in the presence of sufficient QS signal, the AHLs (N-Acyl homoserine lactones). Technologies employed to create the data: Total Internal Reflection Fluorescence, Phase contrast microscopy, Bioengineering, Microfluidics. Schlueter J-P, McIntosh M, Hattab G, Nattkemper TW, Becker A. (2015): Phase Contrast and Fluorescence Bacterial Time-Lapse Microscopy Image Data. Bielefeld University. doi:10.4119/unibi/2777409. Charoenpanich, P., Soto, M. J., Becker, A. , & McIntosh, M. (2015). Quorum sensing restrains growth and is rapidly inactivated during domestication of Sinorhizobium meliloti. Environmental microbiology reports, 7(2), 373-382.
Caste and task allocation in ants

Group living is a widely adopted strategy by many organisms and given the advantages offered by a social lifestyle, such as increased protection from predators or increased ability for resource exploitation, a wide variety of animals have adopted a social lifestyle. Arguably none have done this more successfully than the social insects. Indeed their efficient division of labour is often cited as a key attribute for the remarkable ecological and evolutionary success of these societies. Within the social insects the most obvious division of labour is reproductive, in which one or a few individuals monopolise reproduction while the majority of essentially sterile workers carry out the remaining tasks essential for colony survival. In almost all social insects, in particular ants, the age of a worker will predispose it to certain tasks, and in some social insects the workers vary in size such that task is associated with worker morphology. In this thesis I explore the proximate and ultimate causes of worker and reproductive division of labour in ant societies, which span a range of social complexities. I predominantly focus on both the highly derived leaf-cutting ants – a so-called ‘pinnacle’ of evolution within the social insects, with a complex division of labour and a strong worker caste system – and in the more basal primitive societies of the queenless ponerine dinosaur ants, which can offer an insight in to the evolution of division of labour at the earliest stages of social lifestyles. This work demonstrates the environmental and genetic determinants of division of labour in group-living societies outside of the classical honey bee model system. This is important as it helps us to better understand the broader processes shaping behaviour and phenotype in the animal kingdom.
Levantamento dos insetos e flutuação populacional das pragas que ocorrem na cultura do caupi (Vigna unguiculata (L.) Walp., em Rio Branco (AC).

Levantamentos semanais de insetos na cultura do caupi (Vigna unguiculata (L.) Walp. cv. Cana Verde), utilizando-se armadilha luminosa e rede de varredura, foram realizados na Fazenda Experimental da EMBRAPA-CPAF/ACRE, no periodo de maio/agosto de 1984 a maio/agosto de 1986. Foram capturados 18.165 insetos divididos em 68 especies ou generos, sendo que os principais, com as respectivas epocas de ocorrencia e picos populacionais, sao as que se seguem: Maruca testulalis (Geyer 1832) (la semana de julho); Neocurtilla hexadactyla (perty 1832) (1a semana de junho); Plezodorus guildinii (Westwood 1837) (1a semana de junho); Cerotoma tingomarianus Bechyne (3a semana de junho) e Crinocerus sanctus (Fabr.) (3a semana de julho). Ocorreram ainda, 6 especies de predadores e um taxon, Euschistus sp. , que apresenta potencialidade para se tornar praga da cultura.
Functional and phylogenetic dimensions are more important than the taxonomic dimension for capturing variation in stream fish communities

Biodiversity is inherently multidimensional in nature, differences in evolutionary history, attributes of species, taxonomic composition constitutes a small fraction of whole variation present in this multidimensional space. Despite its multidimensional characteristic, biodiversity has been traditionally measured by assessing its dimensions separately through metrics of diversity. However, assessing multiple dimensions in a common framework opens the possibility of answering interesting questions that, until now, are poorly understood, such as: What dimensions capture most of the variation present in biodiversity among communities? We assess this question by extending the framework of Importance Values (IVs) to three dimensions of variation in biodiversity, functional, taxonomic and phylogenetic, and evaluate which of these captures the most variation in biodiversity space. To address this question we used data from stream fish communities of the Ivinhema River Basin in Brazil. We found that functional and phylogenetic dimensions are more important than the taxonomic dimension (represented by richness) in capturing variation in the biodiversity space formed by these three dimensions together. Furthermore, the IVs of these three dimensions were similar along an altitudinal gradient, indicating similar contributions by a given dimension in different environmental conditions. We highlight the importance of adopting a multidimensional approach when describing biodiversity, since richness (the proxy for taxonomic dimension), despite being the most commonly used, is an incomplete surrogate to capture the variation present in the biodiversity space of stream fish communities.
Chronic Inflammation in Malignant Mesothelioma Pathogenesis: Focus on HMGB1 Isoforms and Germline BAP1 Mutations

Malignant mesothelioma (MM) is an aggressive cancer arising from the mesothelial cells forming the lining of the pleural, pericardial, and peritoneal cavities. Prolonged exposure to carcinogenic mineral fibers, such as asbestos, is the most important risk factor for MM development. Mechanistically, asbestos-induced chronic inflammation is considered a crucial event in MM pathogenesis. High Mobility Group Box 1 (HMGB1) is a pro-inflammatory molecule previously identified as mediator of both asbestos-induced carcinogenesis and MM progression. Here, we show that total HMGB1 levels can reliably distinguish asbestos-exposed individuals and MM patients from healthy controls. Moreover, a specific HMGB1 isoform—hyper-acetylated HMGB1—is significantly increased in MM patients compared to asbestos-exposed individuals and healthy controls. Finally, total and hyper-acetylated HMGB1 can also help differentiating MM patients from patients with pleural effusions due to other causes. Our results suggest that hyper-acetylated HMGB1 might represent a promising novel biomarker for early diagnosis of MM. Continuing our effort to refine the identification of individuals at risk of developing MM, we sought to investigate the role of asbestos exposure in presence of germline mutations in the gene encoding BRCA1 associated protein-1 (BAP1 ), which have been recently reported as predisposing events to MM and several other cancers. However, in individuals with germline BAP1 mutations that developed MM, occupational exposure to asbestos is not usually reported. Here, using a genetically engineered murine model, we discovered
Seasonal dynamics of avian guilds inside and outside core protected areas in an Andean Biosphere Reserve of southern Chile

ABSTRACT Capsule: Many protected forests at high elevations show higher endemic biodiversity than unprotected habitats at low elevations. In seasonal ecosystems, however, harsh environmental conditions during winter may force individuals to move from protected forests to unprotected degraded forests in lowlands. Aims: To examine how forest types and seasons affect avian diversity and habitat-use guilds in protected and unprotected forests. Methods: Habitat and seasonal avian surveys were conducted to test forest type and seasonal differences on avian species richness, relative abundances and relative abundance of habitat-use guilds. Results: Twenty-three avian species (∼40% endemics) were recorded. Highland old growth forests showed the highest richness (4.1–4.9 species/point count). The lowest richness was recorded in mid-elevation secondary forests (3.1 species/point count). The highest relative abundances for habitat-specialist understorey users and large tree users were recorded in highland old growth forests. However, the abundance of large tree users was higher in secondary forests at low elevations during colder seasons. Conclusions: Some species and guilds may move to lower elevations outside protected areas during winter. Increasing degradation of unprotected areas will likely affect the suitability of ‘winter habitat’ for specialist guilds, and thus the ecological processes and source/sink dynamics occurring across boundaries of protected and unprotected areas.