Miracle-dz/UniFAR-FTUs huggingface dataset:
Shifts in vegetation and avian community structure following the decline of a foundational forest species, the eastern hemlock

ABSTRACT Eastern hemlock (Tsuga canadensis) is undergoing widespread decline throughout the eastern United States due to the introduction of the nonnative hemlock woolly adelgid (Adelges tsugae). In light of hemlock's unique significance for avian communities, we examined the long-term response of the breeding bird community to the decline and die-off of this foundational forest species. We conducted variable-radius point counts to survey bird communities in both hemlock and hardwood stands in 2000, during the early stages of adelgid infestation, and again in 2015 and 2016, following significant hemlock decline. We also measured the severity of hemlock decline and associated vegetation variables in the same hemlock stands in which avian surveys were completed. We used multispecies occupancy models to examine species-specific and species group responses to hemlock decline. Results showed that, across hemlock stands, hemlock basal area declined from a mean of 56% of the total basal area to 46%, and that hemlock decline was correlated with current vegetation structure, including an increased deciduous understory. Species richness of hemlock-associated birds declined by an average of ∼1 species per survey location. The Black-throated Green Warbler (Setophaga virens) was the most strongly affected, declining in occupancy by 30%. All other species groups responded positively, with the strongest responses by species associated with the shrub layer, forest edge, and mature deciduous habitat. The species composition in hemlock and hardwood stands became more similar over time as the unique species assemblages in hemlock stands gave way to the avian community of the surrounding hardwood landscape, highlighting a trend toward homogenization of the avian community. Where hemlock-associated bird species persisted, their presence was correlated with a combined effect of greater hemlock basal area and better hemlock condition. Our results demonstrate that the decline of hemlocks has restructured vegetation communities and their associated avian communities over time, with strong implications for forest-specialist birds.
Complete plastome sequence of Erythropalum scandens (Erythropalaceae), an edible and medicinally important liana in China

Abstract Erythropalum scandens (Erythropalaceae, Santalales) is a large liana distributed in alluvial and riparian forests of Southeast Asia. Here we report and characterize the complete plastid genome sequence of E. scandens in an effort to provide genomic resources useful for developing its medicinal and edible value. The complete plastome is 156,154 bp in length and contains the typical structure and gene content of angiosperm plastomes, including two Inverted Repeat (IR) regions of 26,394 bp, a large single-copy (LSC) region of 84,799 bp and a small single-copy (SSC) region of 18,567 bp. The plastome contains 112 genes, consisting of 79 unique protein-coding genes, 29 unique tRNA genes and four unique rRNA genes. The overall A/T content in the plastome of E. scandens is 62.01%. Phylogenetic analyses were performed using the entire plastome, including genes, spacers and introns, which recovered E. scandens as sister to remaining Santalales with complete plastome sequences.
Towards a population approach for evaluating grassland restoration—a systematic review

Persistence of restored populations depends on growth, reproduction, dispersal, local adaptation, and a suitable landscape pattern to foster metapopulation dynamics. Although the negative effects of habitat fragmentation on plant population dynamics are well understood, particularly in grasslands, the population traits that control grassland restoration are less known. We reviewed the use of population traits for evaluating grassland restoration success based on 141 publications (1986–2015). The results demonstrated that population demography was relatively well‐assessed but detailed studies providing information on key stages of the life cycle were lacking despite their importance in determining population viability. Vegetative and generative performances have been thoroughly investigated, notably the components of plant fitness, such as reproductive output, while genetic and spatial population structures were largely ignored. More work on the population effects of ecological restoration would be welcomed, particularly with a focus on population genetics. Targeted species were principally common and dominant natives, or invasive plants while rare or threatened species were poorly considered. Evaluation of ecological restoration should be conducted at different scales of ecological complexity, but so far, communities and ecosystems are over represented, and more focus should be directed towards a population approach as population traits are essential indicators of restoration success.
STAT3 in the Regulation of Brown Adipocyte Differentiation

STAT3 IN THE REGULATION OF BROWN ADIPOCYTE DIFFERENTIATION Marc Cantwell, B.S. A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at Virginia Commonwealth University Virginia Commonwealth University, 2018 Advisor: Andrew C. Larner, M.D., Ph.D. Professor, Department of Biochemistry and Molecular Biology Thermogenic fat is a promising target for new therapies in diabetes and obesity. Understanding how thermogenic fat develops is important to develop rational strategies to treat obesity. Previously, we have shown that Tyk2 and STAT3, part of the JAK-STAT pathway, are necessary for proper development of classical brown fat. Using primary preadipocytes isolated from newborn mice we demonstrate that STAT3 is required for differentiation and robust expression of Uncoupling Protein 1. We also confirm that STAT3 is necessary during the early induction stage of differentiation and is dispensable during the later terminal differentiation stage. Without STAT3, the brown preadipocytes have increased apoptosis early in the terminal differentiation phase. We also show that the block in differentiation is caused by an inability of STAT3 knockouts to down regulate β-catenin by the end of the induction phase. Application of Wnt/β-catenin inhibitors or knockdown of β-catenin during the induction phase is sufficient to fully rescue differentiation of brown adipocytes from the Myf5+ lineage, including reduction in
Factors that influence in Jatropha curcas L. latex production

Latex from Jatropha curcas L. exhibits biotechnological potential for the development of biodiesel and drugs. Little is known about the collection methods and latex productivity of this species. In order to garner information on the use of J. curcas latex, factors that influence production by this species were assessed. As a result, no significant difference was found between the volume of latex collected in the stem and the branches. With respect to environmental characteristics, climatic conditions, such as low temperatures and rainfall, affected production. The period of low temperatures and leaf fall occurs after fruit harvest and, in the absence of strong sinks, the plant can use the assimilates to generate greater latex CROP PRODUCTION AND MANAGEMENT Article Factors that influence in Jatropha curcas L. latex production Fábio Santos Matos1, Angelina Luzia Ciappina1, Ednaldo Candido Rocha1, Luciane Madureira Almeida2* 1.Universidade Estadual de Goiás Departamento de Produção Vegetal Ipameri (GO), Brazil. 2.Universidade Estadual de Goiás Departamento de Ciências Exatas e Tecnológicas Anápolis (GO), Brazil. *Corresponding author: luciane.almeida@ueg.br Received: Nov. 9, 2016 – Accepted: Feb. 28, 2017 production. Multiple regression analysis demonstrated that latex production is positively associated with plant height and negatively associated with fruit production and other variables that maximize it. During the fruiting process the plant uses most of the assimilates for fruit development and a lower percentage to produce secondary compounds, resulting in less availability of these metabolites for latex production. In general, the latex production obtained from this species is low and limits commercial exploitation of this compound, despite its possible pharmacological potential.
Shock and stabilisation following long‐term drought in tropical forest from 15 years of litterfall dynamics

Litterfall dynamics in tropical forests are a good indicator of overall tropical forest function, indicative of carbon invested in both photosynthesising tissues and reproductive organs such as flowers and fruits. These dynamics are sensitive to changes in climate, such as drought, but little is known about the long‐term responses of tropical forest litterfall dynamics to extended drought stress. We present a 15‐year dataset of litterfall (leaf, flower and fruit, and twigs) from the world's only long‐running drought experiment in tropical forest. This dataset comprises one of the longest published litterfall time series in natural forest, which allows the long‐term effects of drought on forest reproduction and canopy investment to be explored. Over the first 4 years of the experiment, the experimental soil moisture deficit created only a small decline in total litterfall and leaf fall (12% and 13%, respectively), but a very strong initial decline in reproductive litterfall (flowers and fruits) of 54%. This loss of flowering and fruiting was accompanied by a de‐coupling of all litterfall patterns from seasonal climate variables. However, following >10 years of the experimental drought, flower and fruiting re‐stabilised at levels greater than in the control plot, despite high tree mortality in the drought plot. Litterfall relationships with atmospheric drivers were re‐established alongside a strong new apparent trade‐off between litterfall and tree growth. Synthesis. We demonstrate that this tropical forest went through an initial shock response during the first 4 years of intense drought, where reproductive effort was arrested and seasonal litterfall patterns were lost. However, following >10 years of experimental drought, this system appears to be re‐stabilising at a new functional state where reproduction is substantially elevated on a per tree basis; and there is a new strong trade‐off between investment in canopy production and wood production.
The Effect Of Crude Protein Halimeda SP. On Cyprinus Carpio Infected Koi Herpes Virus On Expression Of Major Histocompatibility Complex Class-1

Halimeda sp. is a kind species of macroalgae that abundant grow in Indonesia. The utilization of Halimeda especially protein for disease prevention caused by the virus has not been done to the fish. The purpose of the study is to know the treatment of crude protein Halimeda sp on Cyprinus carpio infected by Koi Harvest Virus (KHV) on the expression of Major Histocompatibility Complex (MHC) class 1. MHC class-1 is one of the immune adaptive response on fish like this C. carpio. The methods are isolation of crude protein Halimeda sp, purification of crude protein, Haemagglutination (HA) test and dot blot test. The result shows that the crude protein of Halimeda sp. can produce of adaptive immune response like MHC class 1. MHC class-1 has the function of the immune system for maintenance of virus attacks directly. Responsible of treatment crude protein Halimeda sp. on C. carpio can be showed quantitatively using the dot blot test result. The conclusion is the crude protein of Halimeda sp. able to activate the MHC class I and to inhibit the proliferation of the KHV and maintenance of the fish cell of C. carpio .
A hitchhiker from the beach: the spread of the maritime halophyte Cochlearia danica along salted continental roads

The increase in road networks facilitates the dispersal of many species of plants along roadsides. In these special habitats, the use of deicing salt can provide suitable habitat conditions for the establishment of stress-tolerant halophytes. This study investigates the spread of an alien halophyte Cochlearia danica in continental Europe. This species is native to the Atlantic shores of Europe, has already spread in many countries along roadsides and was recently discovered in Hungary. We performed a literature review to track the European spread of this species, and investigated the Hungarian occurrences in detail. Then we determined the ability of this species to adapt to local soil conditions by means of soil analyses and germination tests using 19 different NaCl concentrations and alkaline soils. To estimate the rate of spread, we estimated the size of the four Hungarian populations in 2016 and 2017, and at the same time we measured the number of flowering stems, number of flowers in an inflorescence, number of seeds per fruit and seed mass. Cochlearia danica is recorded growing along roadsides in eight countries in continental Europe. Literature data indicate a rapid spread of this species along European roads, of 62–65 km/year. In Hungary this species is recorded at four roadside localities characterized by a high soil salt content. The relationship between NaCl concentration and percentage germination followed a sigmoidal curve. Germination tests revealed a significant negative effect of NaCl concentration on germination above 0.5% NaCl, but germination occurred even on extremely saline substrates with a 2% NaCl concentration. The area of the largest Hungarian population decreased by more than 99% and that of the second largest population increased by more than 30% between 2016 and 2017. Even though this species can adapt to high salinity in the soil, these rapid and marked changes in population size indicate that the population dynamics of this species may depend on interactions between the amount of local precipitation and soil type. Our study indicates that we should expect further occurrences of C. danica along roads.
Dry Weight Accumulation, Root Plasticity, and Stomatal Conductance in Rice ( Oryza sativa L.) Varieties under Drought Stress and Re-Watering Conditions

Drought is one of the main factors limiting rice (Oryza sativa L.) productivity and has become an increasingly severe problem in many regions worldwide. Establishing breeding programs to develop new drought-tolerant varieties requires an understanding of the effect of drought on rice plants and the mechanisms of drought tolerance in rice. We conducted a pot experiment to explore growth characteristics, root plasticity, and stomatal conductance in six rice varieties (DA8, Malagkit Pirurutong, Thierno Bande, Pate Blanc MN1, Kinandang Patong, and Moroberekan) in response to different drought stress and re-watering conditions. Drought stress significantly depressed plant growth, root size, and stomatal conductance in all experimental varieties. These negative effects depended on both the variety and the severity of the drought stress treatment. Under moderate drought stress (10 days after drought treatment), growth was less influenced in roots than in shoots. In contrast, there was an opposite trend under severe drought stress (15 days after drought treatment), with growth being more severely affected in roots than in shoots. Rice plants recovered from drought stress in terms of dry matter accumulation, root size, and stomatal conductance after re-watering; however, the recovery pattern differed among varieties. DA8 exhibited the highest dry weight accumulation and root size (root length, root surface area, root volume, fine root length, and thick root length) under well-watered, drought stress, and re-watering conditions. Kinandang Patong showed the highest recovery ability in dry matter accumulation, root length, root surface area, and stomatal conductance after re-watering. Malagkit Pirurutong expressed the poorest recovery ability in dry matter accumulation after re-watering. These three varieties might be selected for further experiments focusing on the mechanisms of drought tolerance and recovery ability in rice.
Annotated plastome of the temperate woody vine Muehlenbeckia australis (G.Forst.) Meisn. (Polygonaceae)

Abstract We assembled the plastome of the temperate, Southern Hemisphere liana Muehlenbeckia australis from high throughput sequencing data (paired-end Illumina reads) generated from total genomic DNA sequencing libraries. M. australis’ chloroplast genome sequence (GenBank: MG604297) is 163,484 bp in length and composed of long single copy (LSC; 88,166 bp) and short single copy (SSC; 13,486 bp) regions flanked by inverted repeats (IR; 30,916 bp each) typical for angiosperms. The plastome includes 131 genes comprising 83 protein-coding genes, 37 transfer RNA genes, eight ribosomal RNA genes, two possible pseudogenes, psbL and rpl23 with internal stop codons, and truncated repeats of ndhF and rps19 at IR boundaries.
The complete mitochondrial genome and phylogenetic analysis of Matuta planipes (Decapoda: Brachyura: Matutidae)

Abstract The complete mitochondrial genome of Matuta planipes was obtained using long and conventional PCR method. The circular genome was 15,760 bp in length, consisting of 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes and a control region. Of the 37 genes, 23 were encoded by the heavy strand, while the others were encoded by the light strand. The genome composition with A + T bias (70.82%) and gene arrangement were largely identical to those observed in most arthropods, such as the mud crab (Scylla paramamosain). The phylogenetic analysis suggested that M. planipes was closest to Ashtoret lunaris. The newly described mitochondrial genome may provide valuable data for phylogenetic analysis for Matutidae.
Role of p38a in lung tumor progression

Los tumores evolucionan al adquirir anormalidades geneticas de manera secuencial, como la activacion de K-Ras y la perdida de funcionalidad de Tp53, que permiten a las celulas transformadas sobrevivir, proliferar, e invadir, asi como acondicionar su microambiente. Simultaneamente, la celulas transformadas tambien han de lidiar con situaciones de estres, incluyendo un metabolismo acelerado, un genoma altamente inestable, o el sistema de vigilancia de las celulas inmunes. Por lo tanto, las celulas cancerosas han de apoyarse en vias de senalizacion no-oncogenicas que les permiten tolerar las deficiencias de los sistemas de control de homeostasis, adaptarse a los nuevos requerimientos funcionales, y monitorizar los cambios en el microambiente para responder de manera apropiada. La via de las p38 MAPK esta intimamente relacionada con la respuesta al estres y es utilizada por las celulas para transducir senales extracelulares y orquestrar las respuestas correspondientes. p38α es el miembro de la familia de p38 MAPK mas ampliamente expresado, y se le han atribuido clasicamente funciones supresoras tumorales gracias a su habilidad para detener el ciclo celular, inducir diferenciacion, y desencadenar procesos apoptoticos. No obstante, hay evidencia de que el nivel de actividad de p38 MAPK podria estar incrementado en varios tipos de tumor humanos y, en algunos casos, se ha correlacionado con una baja supervivencia, lo que sugiere un papel protumoral. En este estudio, hemos observado una correlacion negativa entre los niveles de expresion de p38α y la supervivencia en pacientes de adenocarcinoma pulmonar. Hemos usado un modelo murino de cancer de pulmon inducido por la expresion del oncogen K-Ras para demostrar que, efectivamente, p38α juega un papel dual durante el desarrollo de la carcinogenesis de pulmon. Por una parte, p38α evita la transformacion maligna de las celulas pulmonares epiteliales sanas mediante la induccion de diferenciacion celular. Sin embargo, en las celulas epiteliales pulmonares transformadas, p38α estimula la proliferacion y la secrecion de citocinas inflamatorias que preparan un nicho favorable para la progresion tumoral. p38α tambien juega un rol protumorigenico al promover la vascularizacion del tumor y la immunotolerancia por parte de las celulas mieloides infiltradas. En conjunto, nuestros datos sugieren que la inhibicion de esta via de senalizacion podria ser util en terminos terapeuticos para los casos de adenocarcinoma de pulmon.
The molecular basis of activity-dependent somatosensory cortex development

The murine primary somatosensory cortex (SI) contains discrete cytoarchitectonic units in layer IV called "barrels" that accurately recapitulate the pattern of the mystacial whisker follicles on the facepad. Presynaptic serotonergic and postsynaptic glutamatergic neurotransmission are known to play a crucial role in development of the barrel cortex since mice lacking Nrl or Mglur5 genes fail to form barrels and excessive activation of 5Htlb receptors disrupts barrel formation. However the intracellular mechanisms by which receptor activation is translated into alterations in neuronal phenotype during cortical development are just beginning to be elucidated. The recent characterisation of the major constituents of the postsynaptic density (PSD) from adult rat forebrains (Walikonis et ah, 2000; Husi et al., 2000) has highlighted potential pathways downstream of glutamate receptors (mGluR5 and NMDARs) for mediating cortical development. Targeted molecules are now being screened for a role in barrel development and include Protein Kinase A (PKA) and Synaptic Ras GTPase activating protein (SynGAP). o I Mice that lack Adenylyl Cyclase 1 (AC1), a Ca~ /calmodulin sensitive adenylyl cyclase that can be regulated by 5HT1B, mGluR and NMDA receptors are "barreless", lacking both TCA and cellular segregation in layer 4. Adcyl" {barreless) mutants also have deficits in LTP/LTD at TCA/layer4 synapses and decreased GluR phosphorylation and association with the PSD (Lu et al., 2003). These results led to the hypothesis that LTP/LTD type synaptic plasticity may be required for barrel development (Lu et al., 2003). cAMP-dependent Protein Kinase A (PKA) is a major downstream target of AC1, implicating a possible role for PKA in barrel development. In Chapter 3,1 show that while barrels are present in Prkar2jJ /_ mice, they show significantly reduced cell density ratio between barrel walls and barrel hollows compared to wild-type animals, but normal thalamocortical afferent segregation in the posteromedial barrel subfield. Immunoelectron microscopy confirms that R2p protein is selectively localised to dendrites and dendritic spines. Biochemistry experiments also show that R2|3 associates with the postsynaptic density in a calcium dependent manner. These data clearly show a role for postsynaptic PKA signaling pathways in barrel development and suggest that PKA may not be the principle target downstream of cAMP generated by adenylyl cyclase
Cnidarian cell type diversity revealed by whole-organism single-cell RNA-seq analysis

A hallmark of animal evolution is the emergence and diversification of cell type-specific transcriptional states. But systematic and unbiased characterization of differentiated gene regulatory programs was so far limited to specific tissues in a few model species. Here, we perform whole-organism single cell transcriptomics to map cell types in the cnidarian Nematostella vectensis, a non-bilaterian animal that display complex tissue-level bodyplan organization. We uncover high diversity of transcriptional states in Nematostella, demonstrating cell type-specific expression for 35% of the genes and 51% of the transcription factors (TFs) detected. We identify eight broad cell clusters corresponding to cell classes such as neurons, muscles, cnidocytes, or digestive cells. These clusters comprise multiple cell modules expressing diverse and specific markers, uncovering in particular a rich repertoire of cells associated with neuronal markers. TF expression and sequence analysis defines the combinatorial code that underlies this cell-specific expression. It also reveals the existence of a complex regulatory lexicon of TF binding motifs encoded at both enhancer and promoters of Nematostella tissue-specific genes. Whole organism single cell RNA-seq is thereby established as a tool for comprehensive study of genome regulation and cell type evolution.