Miracle-dz/UniFAR-FTUs huggingface dataset:
Analysis of Poncirus polyandra (Rutaceae) chloroplast genome and its phylogenetic implications

Abstract Poncirus polyandra is a threatened plant in China Now, the complete chloroplast (cp) genome of P. polyandra was assembled. The cp genome of P. polyandra was 160,212 bp in length, it consists of a pair of inverted repeats ((IRa and IRb) regions (27,016 bp) separated by the large single-copy (LSC, 87,407 bp) and small single-copy (SSC, 18,775 bp) regions. The cp genome encodes 105 unique genes, including 70 protein-coding genes, 30 transfer RNA genes, 4 ribosomal RNA genes, and 1 pseudogene. The phylogenetic tree of Rutaceae showed that P. polyandra was clustered together with genus Citrus and Poncirus.
c-Src Controls Mouse Embryonic Osteogenic Differentiation Through Regulation of Stat1 Stability

The protein tyrosine kinase Src is expressed ubiquitously and is involved in differentiation. However, the role of Src in osteogenic differentiation is complex since it has been reported to function both as repressor and activator. Using the small molecule inhibitor PP2, c-Src specific siRNAs, and tet-inducible lentiviral vectors overexpressing constitutively active c-Src, I show cSrc inhibitory role in mouse embryonic stem cells (mESCs) and mouse preosteoblast MC3T3E1s osteogenic differentiation. I further predicted that the increased level of osteogenic differentiation is regulated through Runt-related transcription factor 2 (Runx2). Additional analysis revealed that active c-Src (p-Y416-c-Src) lowers Runx2 nuclear localization and transcriptional activity in mESCs without having any effect on Runx2 expression level. I provide the first evidence linking inhibitory role of c-Src to Runx2 subcellular localization through signal transducer and activator of transcription 1 (Stat1), the cytoplasmic anchoring partner of Runx2. I discovered that higher level of active c-Src increases Stat1 protein half-life by inhibiting Stat1 proteasomal degradation. Therefore, by inhibition of c-Src activity, Stat1 protein level is reduced resulting in less of interaction with Runx2. This in turn increases nuclear localization and transcriptional activity of Runx2. Collectively, my study has defined a new mechanism, by which c-Src activity inhibits transcriptional regulation of osteogenesis.
Status and prospects of gene editing and transgenic in fishes

Recent advances in high throughout DNA sequencing technologies have revolutionized for better understanding of structure-functional relationships of genes in identifying trait-associated transcriptomes and their regulated gene expressions. Subsequent breakthroughs in gene editing technologies such as zinc finger nucleases, transcriptional activator-like effect or nucleases (TALEN) and CRISPR (clustered regularly interspaced short palindromic repeats) determined chromosomal loci so as to understand gene functions in vivo. Such editing technologies are now being implemented in many laboratories due to an affordable cost and easiness of techniques. Targeted gene delivery and disruptions are now not only restricted to standard cell lines or stem cells, but also primary cell lines and nonmodel agriculturally important species. Progress and implications of gene integration and disruptions in food fishes like salmon, carps, etc. will be highlighted. The positive impacts on myostatin gene (negative growth hormone regulator) disruption mediated muscular growth have been documented. Transposon mediated gene integration technologies for value-additions to small indigenous aquarium fishes by expressing attractive fluorescent color genes could be the future of rainbow revolution. Issues linked with further-tuning with regards to improved efficacy and specificity, while reducing offtarget effects of gene editing tools will be addressed. There are health and environmental concerns with genetically modified organisms (GMOs). CRISPR/Cas9 mediated editing generates indels and hence supposed to be free from transgene-nontoxic and non-allergen. Scientific progress regarding to generate genetically modified carps; those could well be cultivated in a confinement and at the same time economically profitable; will be highlighted. Emphasis should be given for transfer these technologies from the laboratory to land for the development of a consumer-friendly sustainable farming system.
Endoconidiogenesis in Endoconidioma populi and Phaeotheca fissurella

Details of the development of endoconidia were basically the same in Endoconidioma populi and Phaeotheca fissurella. In both species, endoconidiogenesis involved (i) subdivision of conidiogenous mother cells by septation to form two to several daughter cells; (ii) accumulation of an electron-dense material between the daughter and mother cell walls; and (iii) separation of the daughter cells by septum schizolysis, accompanied by the dissolution of mother cell wall. Conidiomata of E. populi were unique in having a closed peridium and a locule filled with conidiogenous mother cells and, therefore, we proposed the new term, cleistopycnidium (pl. -a), for this structure. In the cleistopycnidium of E. populi, endoconidiation usually began in the core of the locule and spread outward. Release of endoconidia was by the degeneration of peridial cell walls.
Comparison of BOLD and CBV using 3D EPI and 3D GRASE for cortical layer fMRI at 7T

Purpose Functional MRI (fMRI) at the mesoscale of cortical layers and columns requires both sensitivity and specificity, which can be compromised if the imaging method is affected by vascular artifacts, particularly cortical draining veins at the pial surface. Recent studies have shown that cerebral blood volume (CBV) imaging is more specific to the actual laminar locus of neural activity than BOLD imaging when using standard gradient-echo (GE) EPI sequences. Gradient and Spin Echo (GRASE) BOLD imaging has also shown greater specificity when compared with GE-BOLD. Methods Here we directly compare CBV and BOLD contrasts in high-resolution imaging of the primary motor cortex for laminar fMRI in four combinations of signal labeling, VASO (CBV) and BOLD with 3D GE-EPI and zoomed 3D GRASE image readouts. Results We find that both CBV imaging using EPI-VASO and BOLD imaging using GRASE-BOLD, show similar specificity and sensitivity and are thus useful tools for mesoscopic fMRI in the human cortex. Conclusion These techniques demonstrate sufficient sensitivity and specificity to allow layer-fMRI to be used by neuroscientists in a wide range of investigations of depth-dependent neural circuitry in the human brain.
Characterization of the complete chloroplast genome of Asparagus filicinus (Asparagaceae: Asparagoideae: Asparagus), a traditional Tibetan medicinal plant

Abstract Asparagus filicinus is a traditional medicinal plant with the treatment of pneumonia and cancer, which has been classified as threatened due to habitat destruction and over-harvesting. In this study, its complete chloroplast genome was assembled from the whole genome Illumina sequencing data. The circular genome was 156,674 bp long, containing a large single copy (LSC) region of 85,003 bp and a small single copy (SSC) region of 18,663 bp, which were separated by a pair of 26,504 bp inverted repeat (IR) regions. It encoded a total of 126 genes, including 72 protein-coding genes, 46 tRNA genes and eight rRNA genes. The most of gene species occurred as a single copy, while 17 gene species occurred in double copies. The overall A + T content was 62.4%, while the corresponding values of the LSC, SSC and IR regions were 64.5, 68.4 and 57.1%, respectively. Phylogenetic analysis indicated that A. filicinus was relatively close to two species belonging to the subgenus Asparagus.
Stat2 loss disrupts damage signalling and is protective in acute pancreatitis

Severity of sterile inflammation, as seen in acute pancreatitis, is determined by damage-sensing receptors, signalling cascades and cytokine production. Stat2 is a type I interferon signalling mediator that also has interferon-independent roles in murine lipopolysaccharide-induced NF-κB-mediated sepsis. However its role in sterile inflammation is unknown. We hypothesised that Stat2 determines severity of non-infective inflammation in the pancreas. Wild type (WT) and Stat2−/− mice were injected intraperitoneally with cerulein or L-arginine. Specific cytokine-blocking antibodies were used in some experiments. Pancreata and blood were harvested 1h and 24h after the final dose of cerulein and up to 96h post L-arginine. Whole-tissue phosphoproteomic changes were assessed using label-free mass spectrometry. Tissue-specific Stat2 effects were studied in WT/Stat2−/− bone-marrow chimera and using Cre-lox recombination to delete Stat2 in pancreatic and duodenal homeobox 1(Pdx1)-expressing cells. Stat2−/− mice were protected from cerulein- and L-arginine-induced pancreatitis. Protection was independent of type I interferon signalling. Stat2−/− mice had lower cytokine levels including TNFα and IL-10 and reduced NF-kB nuclear localisation in pancreatic tissue compared to WT. Inhibition of TNFα improved (inhibition of IL-10 worsened) cerulein-induced pancreatitis in WT but not Stat2−/− mice. Phosphoproteomics showed down-regulation of mitogen-activated protein kinase (MAPK) mediators but accumulation of Ser412-phosphorylated Tak1. Stat2 deletion in Pdx1-expressing acinar cells (Stat2flox/Pdx1-cre) reduced pancreatic TNFα expression, but not histological injury or serum amylase. WT/Stat2−/− bone-marrow chimera were protected from pancreatitis irrespective of host or recipient genotype. Stat2 loss results in disrupted signalling in pancreatitis, upstream of NF-κB in non-acinar and/or bone marrow derived cells.
Damage to artificial seedlings across a disturbed Afromontane forest landscape

Seedling mortality is an important demographic bottleneck for forest regeneration, yet the factors influencing recruitment are often poorly characterized across space and time. In African highlands, where extensive patches of previously disturbed forests remain in persistent shrub‐dominated states, patterns of damage to seedlings have not been examined in detail. We used artificial seedlings to determine how (non‐herbivory‐related) damage varies across a fragmented forest landscape in the Bwindi Impenetrable National Park, Uganda. A total of 848 artificial seedlings were established in 106 plots, each with 8 seedlings, across a gradient of environmental factors, including habitat type, topographic position, distance to water, and distance to human activity. We divided damage into that due to vertebrates, plant debris, and unknown agents. From our 16,960 monthly stem assessments, 1,289 damage events were recorded. The mean “seedling” damage per year (± 1 SE) was 59.5 ± 2.3%. Damage was significantly more frequent in sites dominated by short herbs (66.1 ± 3.0) than in sites dominated by shrubs (60.1 ± 2.6) and ferns (47.9 ± 2.7). The mean percentage of damage by each class of agents was 45.8 ± 2.1% for vertebrates, 21.4 ± 2.1% for plant debris, and 3.8 ± 0.6% for unknown agents. These rates surpass those reported in other montane forests, likely reflecting the density of large vertebrates in our site. Our results indicate that most damage to artificial seedlings arises from larger vertebrates but that most spatial variation in this damage reflects the impacts of falling plant debris. These damage processes appear sufficient to constrain the regeneration of tree species in areas where forest cover is patchy and fragmented.
RAPD markers used for the hybrid identification and parents choice in Liriodendron

According to the genetic difference detected by means of RAPD markers, the methods of distinguish among 2 Liriodendron species and their interspecific hybrid were discussed, and the relationship between genetic distances of parents and their hybrids performance were analysed. Of the total 136 bands amplified with 25 10-mer primers, 3 presented in all 5 L. chinense sample trees, but absented in all 5 L. tulipifera sample trees.
A mathematical model of ephaptic interactions in neuronal fiber pathways: Could there be more than transmission along the tracts?

In the past several decades, there has been numerous experimental and modeling efforts to study ephaptic interactions in neuronal systems. While studies on the matter have looked at either axons of the peripheral nervous system or cortical neuronal structures, no attention has be given to the possibility of ephaptic interactions in the white matter tracts of the brain. Inspired by the highly organized and tightly packed geometry of axons in neuronal fiber pathways, we aim to theoretically investigate the potential effects of ephaptic interactions along these structures that are resilient to experimental probing. For that end, we use axonal cable theory to derive a minimal model of a sheet of N ephaptically coupled axons. We numerically solve the equations and explore the dynamics of the system as the ephaptic coupling parameter is varied. We demonstrate that ephaptic interactions can lead to local phase locking between impulses traveling along adjacent axons. As ephaptic coupling is increased, traveling impulses trigger new impulses along adjacent axons resulting in finite size traveling fronts. For strong enough coupling, impulses propagate laterally and backwards, resulting in complex spatio-temporal patterns. While it is common for large scale brain network models to assume the role of brain fiber pathways to be that of mere transmission of signals between different brain regions, our work calls for a closer re-examination of the validity of such a view. The results suggest that in the presence of significant ephaptic interactions the brain fiber tracts can act as a dynamic active medium. Author summary Starting from local circuit theory and the Fitzhugh-Nagumo cable model of an axon, we derive a system of nonlinear coupled partial differential equations (PDE’s) to model a sheet of N ephaptically coupled axons. We also put forward a continuous limit approximation that transforms the model into a field equation in the form of a two-dimensional PDE that allows for the extension of the model to a 3D domain. We numerically solve the equations and explore the dynamic responses as the ephaptic coupling strength is varied. We observe that ephaptic interaction allows for phase locking of adjacent impulses and coordination of subthreshold dynamics. In addition, when strong enough, ephaptic interaction can lead to the generation of new impulses along the axons as well as lateral and backward propagation in the form of traveling fronts and complex spatio-temporal patterns. The transition between different dynamic regimes happens abruptly at critical values of the parameter. We also compare the dynamics of the two models and find good qualitative correspondence in certain parameter regimes. The results put into question the validity of assuming the role of fiber pathways to be that of mere interneuronal transmission and calls for further investigation of the matter.
Disease and insect pest management in organic cucurbit production

iv CHAPTER 1. GENERAL INTRODUCTION . 1 Thesis Organization . 1 Literature Review . 1 Cucurbits . 1 Organic cucurbits . 2 Major pest and disease complexes of cucurbit crops in the Upper Midwest . 3 Bacterial wilt and cucumber beetles . 3 Squash bug and CYVD . 5 Squash vine borer . 6 Organic pest management. 6 Organic weed management and soil health . 12 Case-based teaching . 13 Thesis Objectives. 15 Literature Cited . 15 CHAPTER 2. COMPARISON OF ROW COVER SYSTEMS FOR PEST MANAGEMENT IN ORGANIC MUSKMELON AND ACORN SQUASH . 21 Abstract . 2
The structure of behavioral variation within a genotype

Individual animals vary in their behaviors. This is true even when they share the same genotype and were reared in the same environment. Clusters of covarying behaviors constitute behavioral syndromes, and an individual’s position along such axes of covariation is a representation of their personality. Despite these conceptual frameworks, the structure of behavioral covariation within a genotype is essentially uncharacterized and its mechanistic origins unknown. Passing hundreds of isogenic Drosophila individuals through an experimental pipeline that captured hundreds of behavioral measures, we found correlations only between sparse pairs of behaviors. Thus, the space of behavioral variation has many independent dimensions. Manipulating the physiology of the brain, and specific neural populations, altered specific correlations. We also observed that variation in gene expression can predict an individual’s position on some behavior axes. This work represents the first steps in understanding the biological mechanisms determining the structure of behavioral variation within a genotype.
Effects of light intensity on growth of juvenile Brazilian flounder paralichthys orbignyanus

Most fishes require a minimum threshold light intensity to be able to develop and grow. The aim of this study was to evaluate the effect of light intensity on growth of juvenile Brazilian flounder Paralichthys orbignyanus. Juvenile flounder (1.55 ± 0.03 g) were randomly distributed into twelve 50 L tanks (75 fish per tank). Light intensities tested were 5 (5 ± 1 lux), 180 (176 ± 6 lux), 700 (712 ± 29 lux) and 2000 lux (1,998 ± 64 lux), all in triplicate. Throughout 42 days, fish were fed a commercial feed until satiation. Salinity was maintained at 32 g L-1, temperature at 23 °C, dissolved oxygen at 6.6 mg L-1, pH at 7.8 and un-ionized ammonia at 0.01 mg L-1 NH3-N. At the end of the experiment, juveniles reared at 5 and 180 lux reached respectively 10.1 ± 0.3 and 9.44 ± 0.3 g, their weight was higher than those reared at 700 lux (8.45 ± 0.3 g) and 2000 lux (8.44 ± 0.3 g) (P<0.05). Specific growth rate was higher at 5 lux (4.6 ± 0.2%), compared to 700 lux (4.0 ± 0.1%) and 2000 lux (4.0 ± 0.1%) (P<0.05), while fish reared at 180 lux (4.3 ± 0.1%) did not differ from the other treatments (P>0.05). Survival was 100% at all light intensities tested. It was observed that juvenile Brazilian flounder growth is affected by light intensity, and according to the results obtained, they should be reared at light intensities ranging between 5 and 180 lux.
Mitochondrial genome of Murina shuipuensis (Chiroptera: Vespertilionidae) from Shuifu Village, Guizhou, China (type locality)

Abstract Murina shuipuensis, a small-sized forest bat with distinct bright orange-yellow ventral fur, is only found from its type locality thus far. In this study, a complete mitochondrial genome of a male individual of M. shuipuensis from Shuifu Village, Libo, Guizhou China (type locality) was sequenced using Illumina Hiseq. Total length of its genome is 16,585 bp, including two rRNA genes, 22 tRNA genes, 13 protein-coding genes, and a control region. The general arrangement of genes is similar to the other chiropteran mitochondrial genomes. The phylogenetic inference indicates M. shuipuensis and M. leucogaster have closer phylogenetic relationship than other taxa that deposited in NCBI-nt. The complete mitochondrial genome provides valuable information for further taxonomic and phylogenetic researches.
The complete chloroplast genome of Korean Pyrus ussuriensis Maxim. (Rosaceae): providing genetic background of two types of P. ussuriensis

Abstract Pyrus ussuriensis Maxim. is one of the most important pear species cultivated in Asia, grown in northern China, far-east Russia, Korea, and Japan. Here we completed the chloroplast genome of wild P. ussuriensis collected in Bonghwa-gun, Korea, which was 159,986 bp in length consisting of four subregions: 87,947 bp of large single copy (LSC) and 19,255 bp of small single copy (SSC) regions are separated by 26,392 bp of inverted repeat (IR) regions. The genome contained a total of 130 genes including 85 protein-coding genes, eight rRNAs, and 37 tRNAs. The overall GC content was 36.5% and those in the LSC, SSC, and IR regions were 34.2%, 30.4%, and 42.6%, respectively. Phylogenetic analysis of 14 Pyrus chloroplast genomes provided the diverse genetic background for wild P. ussuriensis populations in Korea by confirming that wild P. ussuriensis sequenced in this study contained Pyrus pyrifolia type plastome. It revealed substantial sequence variations up to 121 single nucleotide polymorphisms and 781 insertions and deletions against another wild accession of P. ussuriensis (P. ussuriensis type) collected in Mt. Hambaek, Korea.
Hawkmoth Pollination Facilitates Long-Distance Pollen Dispersal and Reduces Isolation Across a Gradient of Land-Use Change 1

Abstract Land-use change is among the top drivers of global biodiversity loss, which impacts the arrangement and distribution of suitable habitat for species. Population-level effects include increased isolation, decreased population size, and changes to mutualistic and antagonistic interactions. However, the extent to which species are impacted is determined by life history characteristics including dispersal. In plants, mating dynamics can be changed in ways that can negatively impact population persistence if dispersal of pollen and/or seed is disrupted. Long-distance dispersal has the potential to buffer species from the negative impacts of land-use change. Biotic vectors of long-distance dispersal have been less frequently studied, though specific taxa are known to travel great distances. Here, we describe population genetic diversity and structure in a sphingophilous species that is experiencing habitat fragmentation through land-use change, Oenothera harringtonii W. L. Wagner, Stockh. & W. M. Klein (Onagraceae). We use 12 nuclear and four plastid microsatellite markers and show that pollen dispersal by hawkmoths drives high gene flow and low population differentiation despite a range-wide gradient of land-use change and habitat fragmentation. By separating the contributions of pollen and seed dispersal to gene flow, we show that most of the genetic parameters are driven by hawkmoth-facilitated long-distance pollen dispersal, but populations with small, effective population sizes experience higher levels of relatedness and inbreeding. We discuss considerations for conservation efforts for this and other species that are pollinated by long-distance dispersers.
Integrating palaeontological and molecular data uncovers multiple ancient and recent dispersals in the pantropical Hamamelidaceae

The integration of palaeontological and phylogenetic data can improve our understanding in the spatio‐temporal evolutionary processes of living organisms. However, how best to use fossil data in divergence time estimation and ancestral range reconstruction remains challenging. Here, we integrated palaeontological and molecular data to investigate the historical biogeography of Hamamelidaceae, a pantropical angiosperm family with abundant fossils outside its present distribution.
Nosema ceranae, the most common microsporidium infecting Apis mellifera in the main beekeeping regions of China since at least 2005

The aim of this study was to determine the prevalence and distribution of Nosema spp. in Apis mellifera using historical worker bee samples collected between 2005 and 2010 in China. Out of 292 samples initially analysed by microscopy, 69 were Nosema spore positive. The prevalence of Nosema infections in Southern China (38.9%) was higher than in Central and Northern China (21.9 and 16.7%, respectively). Positive samples were subjected to multiplex PCR amplifications with primers corresponding to 16S rRNA specific sequences of Nosema ceranae and Nosema apis. N. apis was detected in only one sample collected in 2008 in Shandong province, whereas N. ceranae was detected in 68 samples, which indicates that N. ceranae is the most common Nosema species infecting A. mellifera in China since at least 2005.