Miracle-dz/UniFAR-FTUs huggingface dataset:
Effect of combined inorganic with organic acids pretreatment of rice straw on its structure properties and enzymatic hydrolysis

Rice straw was pretreated with sulfuric acid combined with five organic acids (oxalic acid, acetic acid, tartaric acid, succinic acid, and fumaric acid) at 121°C for 90 min with five different blending ratios. The concentrations of glucose, xylose, arabinose and inhibitors such as acetic acid, furfural and HMF (5‐hydroxymethylfurfural) in the prehydrolysate were analyzed. It demonstrated that the concentrations of both sugars and inhibitors in prehydrolysate decreased with increasing organic acids blending ratio. The different solid residues from pretreatments were subjected to enzymatic hydrolysis process. The results showed that pretreating rice straw using combined sulfuric acid with oxalic acid or fumaric acid resulted in the maximum glucose yield (∼66%) after 72 h enzymatic hydrolysis in sharp contrast to ∼58% glucose yield obtained from pretreatment only with sulfuric acid under the same conditions. Furthermore, the structure of the raw material and the pretreated rice straw were characterized by scanning electron microscopy (SEM) and Fourier transformer infrared (FTIR) spectrum to clarify the effects of the combined sulfuric acid with oxalic or fumaric acid pretreatment on disrupting the fibers, removing hemicellulose and making the cellulose structure loose. © 2017 American Institute of Chemical Engineers Environ Prog, 37: 808–814, 2018
Hydroponic cultivation of Physalis angulata L.: growth and production under nitrogen doses1

ABSTRACT RESUMO species, primarily to identify and assess substances with possible medicinal value (Guimaraes et al. 2009, Sa et al. 2011). However, just a few researches have investigated its cultivation or management, including Souza & Amorim (2009), who assessed the growth and development of the species under water deficit, and Cruz et al. (2015), who evaluated the influence of phosphate fertilizer on its cultivation. Nevertheless, much needs to be studied to establish cash crops of the species, particularly in terms of mineral nutrition.Mineral nutrition refers to the supply of nutrients to plants, aimed at increasing yields and 1. Manuscript received in Dec./2016 and accepted for publication in May/2017 (http://dx.doi.org/10.1590/1983-40632016v4744652). 2. Universidade Estadual de Feira de Santana, Departamento de Ciencias Biologicas, Feira de Santana, BA, Brazil. E-mails : leiteromeu@hotmail.com, tamara.tanan@yahoo.com. br, marilzaagro@hotmail.com, lenaldo.uefs@gmail.com, pedro_804@outlook.com. The
Repopulation of Irradiated Mice with Medicinally Stimulating Cells and Infection with Moloney Sarcoma Virus Have a Profound Effect on Regeneration of Splenic Megakaryocytes

The megakaryocyte (Mg) numbers per cross-sectioned spleen slides were arbitrarily evaluated in untreated Balb/cann and C57Bl inbred mouse strains, in sublethally (600 R) and lethally (850 R) irradiated mice and in mice repopulated with syngeneic bone marrow or marrow stromal cell cultures at various time intervals. The impact of Mu-MSV infection or of Mu-MSV induced sarcoma on spleen Mg was also evaluated. Spleens of control mice of both strains harbored numerous Mg. Following sublethal irradiation, severe atrophy of the spleen resulted in the disappearance of Mg from day 6 lasting to day 16. Repopulation with marrow cells lead to the reappearance of Mg by day 8, their proliferation as evidenced by mitosis and full recovery of the population on day 24. Bone marrow stromal cell cultures failed to repopulate irradiated spleens with Mg. C57Bl mice irradiated with 850 R and repopulated with syngeneic bone marrow also recovered their Mg population, although a full recovery required a longer time. Mg in the spleen of Moloney sarcoma virus infected mice or in spleen of mice which developed tumours following local administration of Mu-MSV greatly increased in number by day 18 post infection, and their numbers exceeded those of normal animals, thus the Mu-MSV can be considered as having a positive effect on spleen Mg in rodents.
Further additions to the Bryoflora of Mt. Katahdin, Maine

On August 19, 1963 I had an opportunity to make the ascent of Mt. Katahdin via the Abol Trail, returning by way of the Appalachian Trail, and as a result of this and an earlier partial climb as far as Chimney Pond was able to report the addition of 20 mosses and 2 hepatics to the 86 bryophytes previously known from the mountain (77 reported by Kennedy and Collins, 5 by Lorentz and 4 by Lowe). The following year a second ascent, on August 28, via the Appalachian and Saddle Trails, and a hike up South Turner Mt. (essentially a spur of Katahdin) on Septem ber 1, resulted in the further addition of 21 unrecorded bryophytes (14 Musci and 7 Hepatics) which are here re corded to bring the total now known from Mt. Katahdin up to 129. As with the previous year's collections, a set has been deposited in the U. S. National Herbarium and dupli cates of most have been distributed to several other major herbaria. To avoid repetition of habitat data the species are listed according to collecting sites.
Human‐induced gradients of reef fish declines in the Hawaiian Archipelago viewed through the lens of traditional management boundaries

Large declines in reef fish populations in Hawai‘i have raised concerns about the sustainability of these resources, and the ecosystem as a whole. To help elucidate the reasons behind these declines, a comprehensive examination of reef fish assemblages was conducted across the entire 2500 km Hawaiian Archipelago. Twenty-five datasets were compiled, representing >25 000 individual surveys conducted throughout Hawai‘i since 2000. To account for overall differences in survey methods, conversion factors were created to standardize among methods. Comparisons of major targeted resource species (N = 35) between the densely populated main (MHI) and remote north-western Hawaiian Islands (NWHI) revealed that 40% of these species had biomass in the MHI below 25% of NWHI levels. In total, 54% of the species examined had biomass <50% of NWHI biomass. The moku or district was a basic unit of resource management in pre-contact Hawai‘i and was used as a unit of spatial stratification for comparisons within the MHI. Biomass of resource species was negatively correlated with human population density within moku boundaries, with extremely low biomass in areas with highest human population densities. No such relationship was found for species not targeted by fishing. A number of remote areas with small human populations in the MHI still support high standing stock of fished species, and these areas are likely important refugia for maintaining fisheries production and biodiversity functioning. These results highlight the large gradient of human impacts on fish assemblages across the Hawaiian Archipelago and the potential in using landscape and seascape units, such as those that are watershed and bio-physically-based, when managing in part based on a framework of traditional ecological knowledge.
Phylogenetics and New Approaches to Vaccine Development for West Nile

West Nile virus (WNV) was first isolated in 1937 from a febrile Ugandan woman. WNV now has a worldwide distribution from Australia and India in the east to Europe and the United States in the west. The first human cases of WNV in the United States were detected in New York in 1999. The North American isolates were also found to be highly neuroinvasive and neurovirulent and in many cases leading to mortality or permanent CNS sequelae among humans. WNV was first isolated in Louisiana in 2001. The genome of this virus named LSUAR01was sequenced and a detailed genetic analysis revealed 26 amino acid changes in comparison to the prototypic New York-99 strain. Phylogenetic analysis using Neighbor-joining and the Bayesian approach showed that LSU-AR01 was closely related to a strain isolated from a mosquito in 1999 in Connecticut. This relationship was bolstered by a 58% bootstrap value and a 66% posterior probability by these algorithms respectively. Comparative pathology revealed that the LSU-AR01 was more neurovirulent and neuroinvasive especially at low doses indicating a virus with a competitive edge. Recombinant vesicular stomatitis virus (rVSV) based vaccines cleverly incorporate reverse genetics to recover a recombinant virus expressing a foreign antigen of interest. rVSV vectored vaccines expressing the LSU-AR01 envelope (E) glycoprotein were engineered and administered to mice in a prime-boost approach. The vaccines were able to confer high degree of protection in mice against lethal challenge with highly virulent WNV LSU-AR01. Detailed immunological analyses of immunized mice revealed the production of neutralizing antibody responses. In addition, vaccinated mice generated WNV E glycoprotein specific CD8CD62L IFNγ T cells response against WNV. Recombinant VSV expressing the Simian Retrovirus-2 (SRV-2) gag and Env gene constructs and the Herpes B virus glycoprotein D gene were constructed and characterized in cell culture experiments. The VSV-
A genetic dissection of the interactions between the CbtA toxin of Escherichia coli and the bacterial cytoskeleton

Prokaryotic chromosomal toxin-antitoxin (TA) systems, consisting of a stable toxin and a labile, cotranscribed antitoxin, have been shown to target a number of essential processes in bacteria. The Escherichia coli genome encodes multiple chromosomal TA systems, including a family of three homologous systems, cbtA/cbeA, ykfI/yafW, and ypjF/yfjZ, that targets the bacterial cytoskeleton. Upon overproduction of the CbtA, YkfI, or YpjF toxins, E. coli cells adopt a lemon-like morphology, reminiscent of that seen upon simultaneous inhibition of cell division and cell elongation pathways. Consistent with this observed morphology, previously published work has shown that the CbtA toxin interacts with both the tubulin-homolog FtsZ, the master regulator of cell division, and the actin-homolog MreB, an essential cell elongation factor. Despite these findings, it has not been demonstrated that the interactions of CbtA with MreB and FtsZ are directly responsible for its observed cellular toxicity, nor have any mechanistic details been revealed. The goal of this research was to elucidate the molecular basis for CbtA toxicity by genetically characterizing the interactions between CbtA and its cytoskeletal targets. By means of a transcription-based bacterial two-hybrid system, we can detect interactions between CbtA and both FtsZ and MreB. In Chapter 2 of this dissertation, I describe the isolation and characterization of two CbtA mutants, each of which interacts with only a single cytoskeletal target. CbtAF65S is unable to bind FtsZ, but maintains interaction with MreB, whereas CbtA-R15C exhibits the reverse interaction profile. Morphological observation of cells overproducing each of these variants establishes that the observed effects of CbtA on cell division and cell elongation are genetically separable. I show further that in combination, the substitutions F65S and R15C alleviate the toxicity of CbtA, consistent with the premise that CbtA toxicity depends on its interactions with both FtsZ and MreB. In Chapters 3 and 4, I describe our efforts to map the CbtA-binding determinants on FtsZ and MreB, respectively. Through bacterial two-hybrid studies and the development of a Bacillus subtilis
Cx43 Expression Increases in Response to Increased Cx43 Expression Increases in Response to Increased Temperature Incubation in the Developing Chicken Embryonic Temperature Incubation in the Developing Chicken Embryonic Brain Brain

2017. Cx43 Expression Increases in Response to Increased Temperature Incubation in the Developing Chicken Embryonic Brain. We used the chicken embryo model to examine whether altered incubation temperature during chicken embryo development would alter the protein expression of heat shock protein 70 (hsp70), hsp90, and connexin 43 (cx43) in the brain. We incubated eggs in either optimal (37.6°C, Con), increased (39.6°C, +2), or decreased (35.6°C, -2) temperature conditions until they reached embryonic day 16 (E16). The -2 condition significantly increased incidence of embryonic mortality. As shown in the literature, the development of the eggs was accelerated or decelerated due to increased or decreased temperature respectively. To control for this, we incubated eggs at optimal temperature (37.6°C) to the developmental stage of the +2 (E17.5, HH43-44) and -2 (E12, HH38) conditions. Embryonic chicken brain protein was quantified for hsp70, hsp90, and cx43 using Western Blot analysis. We found that the +2 condition significantly increased cx43 and hsp70 protein expression, but had no effect on hsp90 protein expression.
Salicylic acid induced changes on antioxidant capacity, pigments and grain yield of soybean genotypes in water deficit condition

ABSTRACT Salicylic acid (SA) plays an important role in the regulation of plant growth and development in response to water deficit. The effect of SA (0, 0.4 and 0.8 mM) on some physiological parameters of three soybean genotypes was investigated in three irrigation schedules included (85%, 65% and 45% of field capacity) during 2014–2015. Results showed that water deficit decreased stomatal conductance, leaf area index, relative water content, membrane stability index, yield components and grain yield particularly in L17 genotype. Activities of superoxide dismutase, ascorbate peroxidase and concentration of hydrogen peroxide, proline and total protein were increased in response to water deficit as well as SA applications. SA inhibited catalase activity resulting in increased hydrogen peroxide accumulation in soybean genotypes. Application of 0.4 mM SA decreased the adverse effects of water deficit in soybean genotypes by elevation of antioxidant enzymes activity and reducing malondialdehyde formation especially in Williams genotype.
Defining the Microenvironment for Directing Embryonic Stem Cells into Endothelial Cells - eScholarship

Embryonic stem cells (ESC) are pluripotent cells that boast unlimited expansion potential in vitro and the ability to differentiate into any cell in the adult body. Maturation of ESC into endothelial cells (EC) provides a developmental model and cell source for therapeutic applications. During vascular development, ESC differentiate into vascular progenitor cells (VPC), a multipotent progenitor that may further specialize into EC and SMC daughter cell populations. However, the cues that guide both VPC and EC differentiation during in vitro vascular specification are still not well understood. Here, I report the generation of a specialized cell line for studying vascular development in vitro. Using serum-free protocols, the generation of VPC from this cell line was optimized for generation of VPC and EC based on peak Flk-1 and VE-cadherin expression respectively. The optimization factors were differentiation length, initial cell seeding density, growth factor concentrations, and substrate. In order to examine the role of insoluble vascular endothelial growth factor (VEGF) signaling, cells were exposed to insoluble VEGF bound within fibronectin matrix and assessed for VPC differentiation and Flt-1 expression. To a lesser extent, smooth muscle cell differentiation and the generation of microvascular formations in a three-dimensional (3D) microfluidic device were also investigated. Overall, the specialized cell line expressed green fluorescent protein under the Tie-2 promoter and red fluorescent protein under the α-SMA promoter. These cells generated a high number and a pure population of Flk-1+ cells that later differentiate into EC cells that express VE-cadherin, acetylated low density lipoprotein, and have the ability to form vascular-like structures. When exposed to high levels of vascular endothelial growth factor (VEGF), both soluble and insoluble in combination, Flt-1 was upregulated. During differentiation, initial cell seeding density and matrix signaling were more statistically significant compared to growth factor concentrations on upregulating VE-cadherin expression. These novel findings highlight the roles of cell adhesion molecules involved in cell-cell communication and matrix binding during the endothelial differentiation process.
Time-resolved Interaction Proteomics of the Putative Scaffold Protein GIGANTEA in Arabidopsis thaliana

The large, plant-specific protein GIGANTEA (GI) is involved in many physiological processes, mediating rhythmic, post-translational regulation in part through circadian and light regulation of GI RNA expression. GI binds several proteins implicated in the circadian clock, the control of photoperiodic flowering, and abiotic stress responses, and has co-chaperone activity. By extension, further interaction partners might mediate the less well-understood roles of GI but the number and rhythmicity of these interactors is unknown. Here, we seek potential interactors in a time-specific manner, using quantitative proteomics from a time series study of transgenic Arabidopsis thaliana plants constitutively expressing an epitope-tagged GI protein. Previously-identified, direct and indirect interactors of GI were detected but no further F-box proteins related to known GI partners ZTL/FKF1/LKP2. The predominantly non-rhythmic, interacting proteins were implicated in protein folding or degradation, metabolism and chromatin modification, including a small set of partners shared with other clock-related proteins. A transcription factor homologue that we name CYCLING DOF FACTOR 6 (CDF6) was shown to interact both with GI and the ZTL/FKF1/LKP2 proteins and to control photoperiodic flowering. Our results indicate the biochemical pathways, beyond circadian and flowering regulation, that might be affected by GIGANTEA’s rhythmic, post-translational control. Significance Statement Significance statement of up to two sentences of no more than 75 words total; The GIGANTEA protein of Arabidopsis was known for circadian and flowering functions, mediated by the FKF1/LKP2/ZTL family of GI-interacting, F-box proteins, then for a co-chaperone activity of unknown scope. We performed time-resolved, interaction proteomics, identifying CDF6 (At1g26790) as a morning-specific GI interactor that controls flowering time. Unlike FKF1 and CDF proteins, most of the 240 candidate partners were not rhythmically enriched. They link GI to proteostasis and metabolic functions that might mediate GI’s physiological functions.
Variation of the biotic neighbourhood and topographic effects on tree survival in an old‐growth temperate forest

Question Tree mortality can determine forest dynamics and succession, alter nutrient cycling and contribute to tree species coexistence. Understanding the mechanisms that maintain species diversity is a central goal of community ecology. In this study, we incorporated survival data from a 10-year interval census to determine whether there is significant interspecies variation in the effects of biotic neighbourhood variables and whether there is significant spatial variation in the effects of topographic variables on tree survival in a broadleaved-Korean pine temperate forest. Location A temperate forest in northeast China. Methods We used generalized linear mixed-effects models and geographically weighted generalized linear models as well as their corresponding test approaches to determine whether there is significant interspecies variation in the effects of biotic neighbourhood variables over variable neighbourhood radii and whether there is significant spatial variation in the effects of topographic variables on tree survival across multiple spatial scales in an old-growth temperate forest dynamics plot in northeast China. Results Our results showed that the effects of neighbourhood variables on tree survival varied among species and that those of topography varied over space. However, the results depended on the neighbourhood radius and spatial scale. The neighbourhood radius affected the detection of variation in neighbourhood effects among species, and the spatial scale similarly affected the detection of spatial variation in the effects of topography. The effect of conspecific neighbour density on survival varied more widely among species than that of the average phylogenetic dissimilarity of heterospecific neighbours regardless of the neighbourhood radius. Moreover, the effect of elevation varied more widely over space than those of convexity and hillshade at any quadrat scale. Conclusions Our findings highlight that future studies should account for variations in the neighbourhood radius among species and/or circumstances as well as the spatial scale when assessing the factors that contribute to species coexistence in long-lived organisms. Species leaf phenology, shade and drought tolerance and environmental filtering may explain these variations in the effects of neighbourhood and topographic variables on tree survival. Overall, our results indicate that both density dependence and resource niche partitioning are important mechanisms for maintaining biodiversity in this broadleaved-Korean pine temperate forest. This article is protected by copyright. All rights reserved.
Cardiovascular Fetal Programming in Quail (Colinus virginianus), An Avian Comparative Model

The consequences of early embryonic insults and how they affect subsequent life reflects the emerging concept of "fetal programming". The aim of this project is to study the effects of embryonic insults as they subsequently manifest themselves in adults, with emphasis on the heart and vasculature. My experiments establish that fetal programming operates on the bobwhite quail inducing similar changes as those observed in mammalians and other birds. The quail's fast development provides reliable data in a short period of time than other avian models (e.g. domestic chicken). Data on quail showed a correlation between egg mass and hatchling mass; where small eggs produce small hatchlings but a high mortality made it impractical as a stressor for this study. Hypoxia was used as a stressor during embryonic incubation, where it induced a low hatching weight in quail that was not observable in adult birds. Morphological measurements demonstrated an increased ventricular collagen content and reduced ventricular lumen in birds in adults incubated in hypoxia consistent with hypertension. The hematological analyzes showed few differences indicating organ remodeling instead of hematopoietic compensation. The assessment of vascular reactivity pointed out an impaired endothelium dependent relaxation commonly associated to hypertension in birds and mammals. Fetal programming could be a widespread response to an adverse prenatal environment in endotherms and the resulting data from this work contributes to our understanding of fetal programming in vertebrates and its long term consequences.
New combinations, status, and species of Neotropical Ambrysini (Heteroptera: Naucoridae: Cryphocricinae)

The Neotropical saucer bug species Ambrysus maldonadus La Rivers and Ambrysus montandoni La Rivers originally were placed in Ambrysus Stal despite aberrant physiognomies and features inconsistent with the genus. These two species are herein transferred from Ambrysus to Carvalhoiella De Carlo and are new combinations. Further, Ambrysus (Picrops) usingeri La Rivers represents a monotypic subgenus, which is herein elevated to full generic status. As such, Picrops usingeri represents a new status for this species and a second species of Picrops from the Guiana Shield is described. In addition, the male of Ambrysus brunneus Sites is described and a comparison of character states for genera of Ambrysini is provided.