Miracle-dz/UniFAR-FTUs huggingface dataset:
Pseudomonas syringae evades phagocytosis in animal cells through type III effector-mediated inhibition of the LIM kinase-cofilin system

Certain animal and plant pathogenic bacteria have developed virulence factors (including effector proteins) that enable them to overcome host immunity. A plant pathogen, Pseudomonas syringae pv. tomato (Pto), secretes a large repertoire of effectors into plant cells via a type III secretory apparatus, thereby suppressing plant immunity. Here, we show that exposure to Pto caused sepsis in mice. Surprisingly, the effector HopQ1 disrupted phagocytosis by inhibiting actin rearrangement via a direct interaction with the LIM domain of the animal target protein LIM kinase, a key regulator of actin polymerization. The results provide new insights into cross-kingdom pathogenicity of bacteria. The current studies demonstrate that certain plant pathogenic bacteria such as Pto can be fatal in animals due to cross-kingdom host immune suppression.
Bovine central nervous system development

Ferreira A.O. , Vasconcelos B.G. , Favaron P.O. , Santos A.C. , Leandro R.M. , Pereira F.T. V. , Maria D.A. & Miglino M.A. 2018. Bovine central nervous system development. Pesquisa Veterinária Brasileira 38(1):147-153. Setor de Anatomia dos Animais Domésticos e Silvestres, Faculdade de Medicina Veterinária e Zootecnia, Universidade de São Paulo, Av. Prof. Dr. Orlando Marques de Paiva 87, São Paulo, SP 05508-030, Brasil. E-mail: olivotti@usp.br Central nervous system (CNS) development researches are extremely important to the most common congenital disorders and organogenesis comprehension. However, few studies show the entire developmental process during the critical period. Present research can provide data to new researches related to normal development and abnormalities and changes that occur along the CNS organogenesis, especially nowadays with the need for preliminary studies in animal models, which could be used for experimental research on the influence of viruses, such as the influence of Zika virus on the development of the neural system and its correlation with microcephaly in human newborns. Then, present study describes CNS organogenesis in cattle according to microscopic and macroscopic aspects, identifying structures and correlating to gestational period. Fourteen embryos and nine bovine fetuses at different ages were collected and analyzed. All individuals were measured in order to detect the gestational period. Bovine embryo at 17 days age has its neural tube, cranial neuropore, caudal neuropore and somites developed. After 24 days of development, were observed in cranial part of neural tube five encephalic vesicles denominated: telencephalon, diencephalon, mesencephalon, metencephalon and myelencephalon. In addition, the caudal part of neural tube was identified with the primitive spinal cord. The primordial CNS differentiation occurred from 90 to 110 days. The five encephalic vesicles, primordial spinal cord and the cavities: third ventricule, mesencephalic aqueduct, fourth ventricle and central canal in spinal cord were observed. With 90 days, the main structures were identified: (1) cerebral hemispheres, corpus callosum and fornix, of the telencephalon; (2) interthalamic adhesion, thalamus, hypothalamus and epythalamus (glandula pinealis), of the diencephalon; (3) cerebral peduncles and quadruplets bodies, of the mesencephalon; (4) pons and cerebellum, of the metencephalon; (5) medulla oblongata or bulb, of the myelencephalon; and (6) spinal cord, of the primitive spinal cord. After 110 days of gestation, the five encephalic vesicles and its structures were completely developed. It was noted the presence of the spinal cord with the cervicothoracic and lumbossacral intumescences. In summary, the results describes the formation of the neural tube from the neural plate of the ectoderm, the encephalic vesicles derived from the neural tube and subsequent structural and cavities subdivisions, thus representing the complete embryology of the central nervous system.
Functional Balance between TCF21-Slug defines phenotypic plasticity and sub-classes in high-grade serous ovarian cancer

Cellular plasticity and transitional phenotypes add to complexities of cancer metastasis initiated by single cell epithelial to mesenchymal transition or cooperative cell migration (CCM). We identified novel regulatory cross-talks between Tcf21 and Slug in mediating phenotypic and migration plasticity in high-grade serous ovarian adenocarcinoma. Live imaging discerned CCM as being achieved either through rapid cell proliferation or sheet migration. Transitional states were enriched over the rigid epithelial or mesenchymal phenotypes under conditions of environmental stresses. The Tcf21-Slug interplay identified in HGSC tumors through effective stratification of subtypes also contributed to class-switching in response to disease progression or therapy. Our study effectively provides a framework for understanding the relevance of cellular plasticity in situ as a function of two transcription factors.
Phylogeny and Evolution of the Neotropical Radiation of Lachemilla (Rosaceae): Uncovering a History of Reticulate Evolution and Implications for Infrageneric Classification

Abstract Reticulate evolution often leads to incongruence between nuclear and plastid phylogenies, and comparisons between them have been used as a first approximation to disentangle patterns of hybridization. Because other processes like incomplete lineage sorting and phylogenetic error also produce similar incongruence patterns, additional sources of evidence must be incorporated. Here we focus on reconstructing the phylogeny of Lachemilla (Rosaceae) using nuclear ribosomal ITS and plastid trnL-FDNAsequences, and explore widespread patterns of cytonuclear discordance in this group. Lachemilla is a highly morphologically variable group of perennial herbs and shrubs, and a nearly ubiquitous member of the diverse Neotropical high-altitude grasslands. Our analyses identified four major clades within Lachemilla that are in part congruent with previous morphological classifications of the group. Furthermore, using multiple sources of evidence, including a procrustean approach to cophylogeny estimation, coalescent-based simulations, phylogenetic networks, chromosome counts, and genome size estimations, we also revealed a large-scale pattern of incongruence between the plastid and nuclear phylogenies in Lachemilla, which is mainly the result of widespread hybridization and polyploidy.We also estimated that the origin of Lachemilla in South America (;14.5 MYA) predates the “rapid-uplift” diversification model that has been suggested for other high species-richness Andean plant clades, but following the formation of the high-elevation Andean grasslands during the last 5 MYA, a rapid accumulation of particular nested lineages has contributed to the ubiquitous presence of Lachemilla in these biomes.
Climate Change Trends and Impacts on California Agriculture: A Detailed Review

California is a global leader in the agricultural sector and produces more than 400 types of commodities. The state produces over a third of the country’s vegetables and two-thirds of its fruits and nuts. Despite being highly productive, current and future climate change poses many challenges to the agricultural sector. This paper provides a summary of the current state of knowledge on historical and future trends in climate and their impacts on California agriculture. We present a synthesis of climate change impacts on California agriculture in the context of: (1) historic trends and projected changes in temperature, precipitation, snowpack, heat waves, drought, and flood events; and (2) consequent impacts on crop yields, chill hours, pests and diseases, and agricultural vulnerability to climate risks. Finally, we highlight important findings and directions for future research and implementation. The detailed review presented in this paper provides sufficient evidence that the climate in California has changed significantly and is expected to continue changing in the future, and justifies the urgency and importance of enhancing the adaptive capacity of agriculture and reducing vulnerability to climate change. Since agriculture in California is very diverse and each crop responds to climate differently, climate adaptation research should be locally focused along with effective stakeholder engagement and systematic outreach efforts for effective adoption and implementation. The expected readership of this paper includes local stakeholders, researchers, state and national agencies, and international communities interested in learning about climate change and California’s agriculture.
EPIGENETIC REGULATION OF HIV-1 LATENCY BY HISTONE H3 METHYLTRANSFERASES AND H3K27 DEMETHYLASE

14 CHAPTER 1: INTRODUCTION . 16 HIV INFECTION AND AIDS . 17 AIDS and the discovery of HIV . 17 Classification of HIV . 17 Pathogenesis of HIV-1 . 19 HIV-1 LIFE CYCLE AND STRUCTURE OF HIV-1 . 20 HIV structural proteins . 22 Regulatory proteins of HIV . 26 HIV accesory proteins . 28 EPIGENETICS AND TRANSCRIPTION REGULATION . 31 Transcription on “naked” DNA . 31 DNA, histone and chromatin structure . 31 Epigenetics . 32
Comparison of stimulus-evoked BOLD responses in human and monkey visual cortex

We characterized the blood oxygenation level dependent (BOLD) signal in humans and macaque monkeys by comparing the response in visual cortex to a single checkerboard or two checkerboards, spaced 1.5, 3.0, or 4.5 s apart. We found that the magnitude and shape of the BOLD response to a single checkerboard was similar in the two species. In addition, we found that the BOLD responses summed similarly, and that at an inter-stimulus interval (ISI) of 4.5 sec BOLD summation was nearly linear in both species. When comparing the ratio of the amplitude of the response to the second checkerboard at the 4.5 sec ISI with that of the single checkerboard between subjects in both species, the results from both monkey subjects fell within one standard deviation of the mean human results (human mean (n=12): . 95 +/− . 31 second/single response amplitude; monkey 1: 1.16; monkey 2: . 86). At the shorter ISIs, both species demonstrated increased suppression of the BOLD response to the second checkerboard. These findings indicate that the magnitude of the BOLD response to events separated by 4.5 seconds can be accurately measured in and compared between human and monkey visual cortex.
Spring migratory routes and stopover duration of satellite-tracked Eurasian Teals Anas crecca wintering in Italy

Identifying an organism ’ s migratory strategies and routes has important implications for conservation. For most species of European ducks, information on the general course of migration, revealed by ringing recoveries, is available, whereas tracking data on migratory movements are limited to the largest species. In the present paper, we report the results of a tracking study on 29 Eurasian Teals, the smallest European duck, captured during the wintering period at three Italian sites. The departure date of spring migration was determined for 21 individuals, and for 15 the entire spring migratory route was recon-structed. Most ducks departed from wintering grounds between mid-February and March following straight and direct routes along the Black Sea-Mediterranean ﬂ yway. The breeding sites, usually reached by May, were spread from central to north-Eastern Europe to east of the Urals. The migratory speed was slow (approximately 36 km/day on average) because most birds stopped for several weeks at stopover sites, mainly in south-eastern Europe, especially at the very beginning of migration. The active ﬂ ight migration segments were covered at much higher speeds, up to 872 km/day. Stopover duration tended to be shorter when birds were closer to their breeding site. These results, based on the largest satellite tracking effort for this species, revealed for the ﬁ rst time the main features of the migratory strategies of individual Teals wintering in Europe, such as the migration timing and speed and stopover localization and duration. is
Endotoxin Tolerance Induced by Different TLR Ligands

Endotoxin tolerance is a long-recognised property of macrophages that leads to an altered response to repeated or chronic exposure to Toll-like receptor (TLR) ligands. The physiological role of tolerance is to limit the potential damage to host tissue that may otherwise result from prolonged production of pro-inflammatory cytokines. Endotoxin tolerance is induced by all TLRs tested to date, however, tolerance induced by the TLR4 ligand lipopolysaccharide (LPS) is by far the best studied. LPS tolerance involves a global transcriptional shift from a pro-inflammatory response toward one characterised by the expression of anti-inflammatory and pro-resolution factors. Although largely reversible, LPS-tolerance leads to a hybrid macrophage activation state that is pro-inflammatory in nature but possesses distinct regulatory anti-inflammatory features. Remarkably, a comparative transcriptomic analysis of tolerance induced by different TLR ligands has not previously been reported. Here we describe the transcriptomic profiles of mouse macrophages tolerised with ligands for TLR2, TLR3, TLR4 and TLR 9. While we identified TLR-specific transcriptional profiles in macrophages tolerised with each ligand, tolerance induced by TLR4 was the most comprehensive state, such that each gene tolerised by any of the TLRs tested was also found to be tolerised by TLR4. Pro-inflammatory cytokines are not universally supressed in all tolerant cells but distinct patterns of cytokine expression distinguished TLR-specific tolerance. Analysis of gene regulatory regions revealed specific DNA sequence motifs associated with distinct states of TLR tolerance, implicating previously identified as well as novel transcriptional regulators of tolerance in macrophages. These data provide a basis for the future exploitation of TLR-specific tolerant states to achieve therapeutic re-programming of the innate immune response.
Genome analyses show strong selection on coloration, morphological and behavioral phenotypes in birds-of-paradise

Abstract The diverse array of phenotypes and courtship displays exhibited by the birds-of-paradise have long fascinated scientists and laymen alike. Remarkably, almost nothing is known about the genomics of this iconic radiation. There are 41 species in 16 genera currently recognized within the birds-of-paradise family (Paradisaeidae), most of which are endemic to the island of New Guinea. In this study, we sequenced genomes of representatives from all five major clades within this family to characterize genomic changes that may have played an important role in the evolution of the group’s extensive phenotypic diversity. We found genes important for coloration, morphology and feather development to be under positive selection. GO enrichment of positively selected genes in the birds-of-paradise showed an enrichment for collagen, glycogen synthesis and regulation, eye development and other categories. In the core birds-of-paradise, we found GO categories for ‘startle response’ (response to predators) and ‘olfactory receptor activity’ to be enriched among the gene families expanding significantly faster compared to the other birds in our study. Furthermore, we found novel families of retrovirus-like retrotransposons active in all three de novo genomes since the early diversification of the birds-of-paradise group, which could have potentially played a role in the evolution of this fascinating group of birds.
Aspects of the ecology and biology of the isopod, Exosphaeroma hylocoetes, (Barnard, 1940) in three temporarily open/closed southern African estuaries

ii ACKNOWLEDGEMENTS . iv LIST OF FIGURES . viii LIST OF TABLES . xii PREFACE . xiv DECLARATION. xv CHAPTER 1: INTRODUCTION AND RATIONALE FOR STUDY. 1 1.1 General Features and Habitats of Isopods . 1 1.2 Isopod Taxonomy and Systematics . 4 1.3 Isopod Life Histories . 8 1.4 South African Estuaries . 10 1.4. 1 Temporarily open/closed estuaries (TOCE’s) . 12 1.4. 1.1 Hydrodynamics . 12 1.5 Ecology of South African Isopods. 18 1.6 Structure of Thesis . 20 CHAPTER 2: THE STUDY SITES. 22 2.
Description of Peridiniopsidaceae, fam. nov. (Peridiniales, Dinophyceae)

The vast majority not only of dinophytes, but also of Peridiniales, live in the marine environment, and some 350 (out of ca 2.500) species are present in freshwater habitats (Mertens et al. 2012). Many freshwater Peridiniales constitute small and only distantly related species groups embedded in predominantly marine clades (e.g., Apocalathium , Chimonodinium , Naiadinium in the Thoracosphaeraceae; species assigned to “ Peridiniopsis ” in the Kryptoperidiniaceae; Zhang et al. 2011b, Gottschling & Sohner 2013, Annenkova et al. 2015; Fig. 1). However, the most distinguished freshwater group of the Peridiniales are the Peridiniaceae including the type species, Peridinium cinctum , and other frequently encountered species such as Peridinium bipes , Peridinium volzii and Peridinium willei .
Environment is more relevant than spatial structure as a driver of regional variation in tropical tree community richness and composition

ABSTRACT Background: Understanding how factors related to environment and geographical distance explain community variation allows insights about how ecological niche and neutral processes control tropical community assembly. Aims: Quantify how variation in regional tree community richness and composition in a humid tropical forest across a mountain chain are related to niche and putative neutral processes. Methods: We used a variation partitioning routine based on Redundancy Analysis to model tropical tree community richness and composition within three distinct elevation belts, as a function of environment and spatial structure, using data from 32 studies in the Serra do Mar Range, south-eastern Brazil. Results: Environmental effects were greater than spatial structure effects to explain community variation in the three elevation belts. There was a trend of decreasing spatial structure effects while environmental effects remained constant from lower to higher elevations. Patterns were congruent for species richness and composition. Conclusions: We suggest that on tropical mountains, niche-related processes are equally relevant for tropical forest community assembly at all elevations, while neutral processes become weaker towards higher elevations. Determining if this trend is a consequence of the greater heterogeneity of environmental conditions associated with higher elevations in tropical mountainous terrain remains an important area of research.
Bacaba-de-leque (Oenocarpus distichus): A new wet tropics nutritional source

The present study aims to determine the nutritional composition of soluble and insoluble fibers, vitamins and minerals in the fruit of bacaba-de-leque (Oenocarpus distichus Mart.) a native Central Amazonian tropical fruit. Results show the fiber contents to be 3.95 g 100 g-1, 100% of which shows to be insoluble fibers. Potassium stood out among the minerals, with 173.85 mg 100 g-1. High vitamin E concentration (6.65 mg 100 g-1) was observed as well. Considering the fruit’s nutritional potential, we suggest its incorporation into the Amazonian population diet as an essential nutrient and health improving compounds source, to be more frequent. Key words: Fiber, vitamins, minerals, nutrition.
Morphometrics of the dwarf honey bee Apis florea show biogeographic differentiation across India

The Asian dwarf honey bee ( Apis florea ) is a relatively small honey bee, nests in the open with single combs attached to tree branches, and inhabits areas uninhabitable to other Apis species. A. florea is one of few honey bees in the genus to have remained unmanaged by beekeepers across Asia. Because A. florea has not been bred for specific traits or transported intentionally across continents like managed Apis species, populations of A. florea should offer insight into natural adaptations of honey bee populations to diverse climates. We use morphometrics to examine which environmental factors correlate with morphological differences between populations of A. florea surveyed across India. The surveyed populations show a trend of increased wing size going from the equator to the north. The populations also vary in Cubital Index, a wing venation measurement often associated with subspecies differentiation, and this variation is correlated with minimum temperature of the coldest month. Taken together, these findings show that A. florea differs morphologically across a temperature gradient in
The influence of subjective sleep quality on the association between eveningness and depressive symptoms

Abstract Increasing evidence suggests that eveningness is associated with increased risk for depression. Eveningness, however, is also associated with poor sleep quality and the unique role of eveningness in depressive symptomatology remains to be elucidated. The goal of the current study, therefore, was to examine the inter-relationships between eveningness, subjective sleep quality and depressive symptoms in healthy participants free of current or previous depression and sleep disorder. Here, 167 healthy participants (mean age 24.16, 129/38 females/males) completed the reduced Morningness–Eveningness Questionnaire (rMEQ), the Pittsburgh Sleep Quality Index (PSQI) and the Centre for Epidemiological Studies Depression Scale (CES-D). Bootstrap mediation analysis for a simple mediation model including rMEQ, PSQI and CES-D was applied. Eveningness was associated with increased depressive symptoms and mediation analysis showed that this relationship was partly mediated by sleep quality. Our results suggest that indicators of depression observed in evening-type individuals cannot be attributed exclusively to disturbed sleep. We suggest that interventions that target both sleep quality and dysfunctional cognitive styles would be optimal to promote well-being in evening-type individuals.
Excision of a selectable marker in transgenic lily (Sorbonne) using the Cre/loxP DNA excision system

Li, S. H. , Du, Y. -P., Wu, Z. H. -Y. , Huang, C. -L. , Zhang, X. -H. , Wang, Z. H. -X. and Jia, G. -X. 2013. Excision of a selectable marker in transgenic lily (Sorbonne) using the Cre/loxP DNA excision system. Can. J. Plant Sci. 93: 903-912. To generate transgenic lily plants with no selectable marker and improved tolerance to abiotic stress, two vectors were co-transformed into the Lilium oriental hybrid Sorbonne by particle bombardment. The pKSB vector included the Cre/loxp-mediated site-specific cDNA excision system under control of the inducible promoter rd29A, and the pBPC-P5CS-F129A vector carried the P5CS gene, which we hypothesized would improve resistance to drought and salt stresses in transgenic lily plantlets. The presence of the two genes was simultaneously detected by PCR and Southern blotting in two resistant plantlets. The co-transformation rate was 0.16%. Subsequently, inducer expression was tested under varying conditions to optimize the deletion of marker gene. Results from molecular detection assays revealed that maintaining bases of bulblet scales at 4°C for 12 h resulted in an increase in the excision rate, reaching 60%. Expression of P5CS improved resistance to salt stress in transgenic lily plantlets. These results demonstrated the feasibility of using the Cre/loxP-based marker elimination system to generate marker-free transgenic plantlets with improved stress tolerance.