Miracle-dz/UniFAR-FTUs huggingface dataset:
General spatial spectral variation in rocky intertidal communities from three biogeographical regions

Understanding general spatial patterns of multiple species is a central aim of biogeography. Spatial analyses of coastal marine assemblages have shown an emergent pattern in that the variability in population abundances increases with increasing spatial scale of observation; i.e. a “red” spectrum of variation in population abundances. However, the generalization of these patterns to other ecological levels and across biogeographical regions remains unexplored. Here, we evaluate the consistency of a reddened relationship between the scale of observation and the variance in ecosystem properties in sessile intertidal rocky‐shore assemblages across three biogeographical regions.
Estudio de la microbiota de vías respiratorias en pacientes pediátricos con fibrosis quística mediante secuenciación masiva y su relación con distintas variables clínicas

La aplicacion de las tecnicas de secuenciacion masiva ha relevado un complejo ecosistema de bacteriano en las vias respiratorias inferiores. En enfermedades pulmonares cronicas, como la fibrosis quistica (FQ) el estudio de la microbiota suscita interes para correlacionar el estado de la enfermedad con cambios en la composicion y diversidad de las comunidades bacterianas. El objetivo del estudio fue describir la composicion de la microbiota, el numero absoluto de especies, su diversidad y la abundancia relativa en muestras de esputo inducido de pacientes pediatricos con FQ y relacionarlo con una serie de variables clinicas de su enfermedad. Para ello se llevo a cabo un estudio observacional transversal de la microbiota de muestras de esputo inducido obtenido de ninos con FQ. Tras la extraccion y depuracion del DNA bacteriano de las muestras de esputo, se procedio a secuenciacion masiva del DNA mediante el sistema Illumina® MiSeq con 250bp pair-ends. Se obtuvieron las secuencias del 16S usando los programas ssu-align y meta-rna. Se determino: Composicion del microbioma: la abundancia absoluta y relativa de especies y dominancia. Alfa diversidad a traves del indice de Shannon Wiener. Beta diversidad mediante el analisis de componentes principales (ACP). Finalmente se realizo un analisis estadistico entre las variantes clinicas de cada paciente y los distintos indices de diversidad bacteriana. RESULTADOS Se analizaron 13 muestras de esputo de ninos con FQ, con edades entre 7 y 17 anos. En todos estaba identificada la mutacion del gen CFTR y todos presentaban la insuficiencia pancreatica. Los generos aislados mediante secuenciacion masiva en la totalidad de pacientes fueron Staphylococcus spp, Streptococcus spp, Granulicatella spp, Gemella spp y Rothia spp. El ACP entre las 13 muestras mostro la existencia de 3 grupos diferenciados. El grupo con mayor densidad de Staphylococcus spp, y menor Actinomyces spp y Streptococcus, presentaba menor diversidad alfa expresada por el Indice de Shanon (p=0,009). Se observo una relacion inversamente proporcional entre la diversidad bacteriana y el deterioro de la funcion respiratoria expresado por la FEV1, aunque no fue estadisticamente significativa. CONCLUSIONES Como en otros estudios, el analisis realizado en nuestros pacientes relevo la presencia de anaerobios obligatorios y otras especies no descritas como patogenos clasicos en FQ. Se ha de determinar el papel de estas especies en la evolucion de la enfermedad. En nuestro estudio, el hallazgo de un microbioma con escasa diversidad, dominado por Staphylococcus se asocio a una peor funcion pulmonar, sin que esta observacion guardara relacion aparente con otras variables clinicas.
Beyond boxes and arrows: Putting the ?bio? into biogeochemistry

The Gaia hypothesis proposes that the earth can be viewed as a single living entity. While this idea remains controversial, there is no doubt that the biotic and abiotic components of the earth are intimately linked in complex webs of chemical reactions collectively described as biogeochemistry. Microbes are the catalysts of most such reactions, but despite their importance, there is a tendency to oversimplify microbial contributions using boxes (compounds) and arrows (reactions). In this brief review, I will highlight recent research that looks beyond the boxes and arrows to the microbes themselves, and describe some examples where the activities of biogeochemical microbes and enzymes have been harnessed for environmental benefits.
Mitochondrial Biology: RNA Import and Xenomitochondrial Compensatory Mechanisms

ii Acknowledgments. iv Dedication . v List of Tables . ix List of Figures . x List of Abbreviations . xii Foreword . 1 Chapter 1 – Literature review . 2 Section 1 – Mitochondrial biology . 2 Section 2 – Animal models of mitochondrial disease . 4 History of xenomitochondrial mice . 4 Section 3 – RNA import into mitochondria . 7 Protists . 8 Plants . 9 Yeast . 10 Mammals . 11 Section 4 – Mechanism of mitochondrial RNA import in mammals . 17 Chapter 2 – Compensatory mechanisms in xenomitochondrial mice . 23 Section 1 – Introduction . 23 Section 2 – Materials and methods . 24
SUPPRESSION OF ANTI-TUMOR IMMUNITY IN CHRONIC LYMPHOCYTIC LEUKEMIA VIA INTERLEUKIN-10 PRODUCTION

OF DISSERTATION SUPPRESSION OF ANTI-TUMOR IMMUNITY IN CHRONIC LYMPHOCYTIC LEUKEMIA VIA INTERLEUKIN-10 PRODUCTION The most common human leukemia is B-cell chronic lymphocytic leukemia (B-CLL), which is characterized by a progressive accumulation of abnormal Blymphocytes in blood, bone marrow and secondary lymphoid organs. Typically disease progression is slow, but as the number of leukemic cells increases, they interfere with the production of other important blood cells, causing the patients to be in an immunosuppressive state. To study the basis of this immunoregulation, we used cells from the transgenic Eμ-TCL1 mouse, which spontaneously develop B-CLL due to a B-cell specific expression of the oncogene, TCL1. Previously we showed that Eμ-TCL1 CLL cells constitutively produce an anti-inflammatory cytokine, IL-10. Here we studied the role of IL-10 in CLL cell survival in vitro and the development of CLL in vivo. We found that neutralization of IL-10 using anti-IL-10 antibodies or blocking the IL-10 receptor (IL-10R) using anti-IL-10R antibodies did not affect the survival of CLL cells in vitro. On the other hand, adoptively transferred Eμ-TCL1 cells grew at a slower rate in IL-10R KO mice vs. wild type (WT) mice. There was a significant reduction in CLL cell engraftment in the spleen, bone marrow, peritoneal cavity and liver of the IL-10R KO compared to WT mice. Further studies revealed that IL-10 could be playing a role in the tumor microenvironment possibly by affecting anti-tumor immunity. This was seen by a reduction in the activation of CD8 T cells as well as a significantly lower production of IFN-γ by CD4 T cells purified from CLLinjected WT mice compared to those purified from CLL-injected IL-10R KO mice. Also CLL-primed IL-10R null T cells were more effective than those from similarly CLL-primed wild type mice in controlling CLL growth in immunodeficient recipient mice. These studies demonstrate that CLL cells suppress host anti-tumor immunity via IL-10 production. This led us to investigate possible mechanisms by which IL-10 is produced. We found a novel role of B-cell receptor (BCR) signaling pathway in constitutive IL-10 secretion. Inhibition of Src or Syk family kinases reduces the constitutive IL-10 production by Eμ-TCL1 cells in a dose dependent manner. We identified the transcription factor Sp1 as a novel regulator of IL-10 production by CLL cells and that it is regulated by BCR signaling via the Syk/MAPK pathway.
Identificação de enteropatógenos em bezerros búfalos, com e sem diarréia, do Vale do Ribeira, Estado de São Paulo, Brasil

Foram avaliados semanalmente, por um periodo de seis semanas, os exames parasitologicos de amostras fecais, diarreicas e nao-diarreicas, de 106 bezerros bufalos, com 3 a 45 dias de idade, provenientes do Vale do Ribeira-SP. Para os exames bacteriologicos e virologicos, foram colhidas amostras fecais de todos os bufalos diarreicos, e igual amostragem de animais sem diarreia. Amostras de sangue foram colhidas dos bufalos neonatos, entre o terceiro e decimo dias de idade, para determinacao dos niveis de imunoglobulina G (IgG). Nos exames parasitologicos, verificou-se a maior ocorrencia de Eimeria spp, Strongyloides papillosus e Toxocara vitulorum. Dentre os agentes bacterianos, observou-se maior frequencia da Escherichia coli (E. coli), Enterobacter cloacae e Klebsiella pneumoniae (isolados ou em associacao). Detectou-se a enterotoxina STa em 5 das 34 amostras de E. coli isoladas de bufalos com diarreia. A norfloxacina, cloranfenicol e gentamicina foram os antimicrobianos mais efetivos frente aos microrganismos isolados. Nenhuma das amostras apresentou bandeamento caracteristico para rotavirus, a partir da tecnica de eletroforese em gel de poliacrilamida. Nao foi constatada nos animais examinados a associacao entre a ocorrencia de diarreia e baixos niveis de IgG serica.
The effect of single nucleotide polymorphisms and mutations on congenital thrombotic thrombocytopenic purpura phenotype

Thrombotic thrombocytopenic purpura (TTP) is a rare, life-threatening disease with a reported incidence of 6 cases per million per year in the UK. It is characterised by episodes of microangiopathic haemolytic anaemia and thrombocytopenia, with the widespread presence of platelet-rich thrombi in the microcirculation, leading to end-organ damage. TTP is a clinically heterogeneous disorder caused by autoantibody inhibition or clearance or by a deficiency in activity or secretion of the von Willebrand factor cleaving protease (ADAMTS13). Over 100 mutations have been identified in ADAMTS13 yet, in some cases, these mutations in congenital TTP alone do not explain the disease phenotype, particularly in late-onset congenital TTP. One aim of this study was to analyse the effect of single nucleotide polymorphisms (SNPs), in conjunction with ADAMTS13 mutations, which have been identified in a cohort of TTP patients with varied clinical phenotype. Twenty mutant expression plasmids containing an ADAMTS13 mutation and/or SNP have been constructed by site-directed mutagenesis (SDM). Fourteen plasmids contained a new non-synonymous mutation (C3484T) which has been rectified by further SDM. After full sequencing of the plasmid ADAMTS13 insert, 24 clones were identified as viable and the resultant protein was expressed in HEK293T cells and analysed by Western blot and ADAMTS13 antigen ELISA. Blots were scanned by densitometry and the intensity of the protein species corresponding to ADAMTS13 determined using ImageJ. The predicted effects of mutations and/or SNPs were annotated by the in silico computational tools SIFT, PolyPhen2, I-Mutant 2.0 and SNPEffect 4.0. Results from this genotype study were compared to clinical phenotype by correlating data held within the TTP Registry at University College London. The resultant analysis showed the mutations located in the N-terminal end of ADAMTS13 protein induced more secretory defects and SNPs had less of an effect on phenotype. The p.R7W and p.A1033T SNPs showed more of an effect on secretion of ADAMTS13 when the mutation was located in the Cterminal end (p.R1060W) which is associated with late-onset phenotype. However, other environmental factors such as changes in the ADAMTS13-VWF axis during pregnancy and infection make a correlation between genotype and phenotype in TTP more challenging.
Expression and functional analysis of SOX3 in murine neurogenesis.

Polyalanine expansions in transcription factors have been associated with eight distinct congenital human diseases. It is thought that in each case the polyalanine expansion causes misfolding of the protein that abrogates protein function. Misfolded proteins form aggregates when expressed in vitro; however, it is less clear whether aggregation is of relevance to these diseases in vivo. To investigate this issue, we used targeted mutagenesis of embryonic stem (ES) cells to generate mice with a polyalanine expansion mutation in Sox3 (Sox3-26ala) that is associated with X-linked Hypopituitarism (XH) in humans. By investigating both ES cells and chimeric mice, we show that endogenous polyalanine expanded SOX3 does not form protein aggregates in vivo but rather is present at dramatically reduced levels within the nucleus of mutant cells. Importantly, the residual mutant protein of chimeric embryos is able to rescue a block in gastrulation but is not sufficient for normal development of the hypothalamus, a region that is functionally compromised in Sox3 null embryos and individuals with XH. Together, these data provide the first definitive example of a disease-relevant PA mutant protein that is both nuclear and functional, thereby manifesting as a partial loss-of-function allele. Citation: Hughes J, Piltz S, Rogers N, McAninch D, Rowley L, et al. (2013) Mechanistic Insight into the Pathology of Polyalanine Expansion Disorders Revealed by a Mouse Model for X Linked Hypopituitarism. PLoS Genet 9(3): e1003290. doi:10.1371/journal.pgen. 1003290 Editor: Sally Camper, University of Michigan, United States of America Received July 12, 2012; Accepted December 16, 2012; Published March 7, 2013 Copyright: 2013 Hughes et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Funding: This work was supported by the Australian Health and Medical Research Council (http://www.nhmrc.gov.au/). PT is a Pfizer Australia Research Fellow. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Competing Interests: PT is supported by a Fellowship from Pfizer Australia. This does not alter the authors’ adherence to all the PLOS Genetics policies on sharing data and materials. * E-mail: paul.thomas@adelaide.edu. au
Determinate or indeterminate growth? Revisiting the growth strategy of sea turtles

Fieldwork was supported by the British Associate of Tortoise Keepers, British Chelonia Group, British High Commission in Cyprus, British Residents Society, Carnegie Trust for the Universities of Scotland, Darwin Initiative, Erwin Warth Foundation, Friends of SPOT, Glasgow Uni versity Court, Kuzey Kibris Turkcell, MEDASSET UK, and Natural Environment Research Council.
Singing through winter nights: Seasonal and diel occurrence of humpback whale (Megaptera novaeangliae) calls in and around the Gully MPA, offshore eastern Canada

Humpback whale use of areas off eastern Canada is poorly understood, a knowledge gap that could impact future conservation efforts. We describe the acoustic occurrence of humpback whales in and around the Gully Marine Protected Area (MPA), an eastern Scotian Shelf submarine canyon. Near-continuous acoustic recordings sampling at 16 kHz were collected from the MPA and nearby slope areas from October 2012 to September 2014 using near-bottom recorders. In an offshore region where humpbacks were thought to be rare, we observed calls from October to June with a peak in song and nonsong calls in December and January. This suggests that some individuals occur in Canadian waters in winter and the Gully region may be a North Atlantic humpback whale migratory corridor. Calls were predominantly songs indicating potential mating activities. Song and nonsong calls occurred more at sunset and during hours of darkness than during daylight. This study improves our understanding of the seasonal occurrence of humpback whales on the Scotian Slope and, more specifically, their use of an offshore protected area.
Regulation of Insulin Sensitivity by Phosphorus

Dietary phosphorus excess as a result of the ever growing consumption of highly processed foods has been associated with developments of ageing related diseases such as diabetes and obesity in the general human population. Insulin resistance is the main feature of aged human population especially in patients with type 2 diabetes and some people with obesity. Thus, the study of a low phosphorus diet on glucose homeostasis such as insulin resistance and glucose tolerance is of great interest. Here, we investigated glucose homeostasis in male and female 129Sv mice fed with low phosphorus diet (0.2% of Pi) vs. control diet (0.4% of Pi). Interestingly, the fasting basal glucose level dropped significantly in male mice after being fed with low Pi diet for 4 weeks. In addition, low Pi diet significantly enhanced insulin sensitivity in both male and female mice. Furthermore, low Pi diet lowered serum Pi levels in mice of both genders without interrupting the growing pattern of body weights during the 10-week feeding period. Examination of proteins with Western Blot revealed that low Pi diet significantly enhanced insulin receptor β (IRβ) levels in skeletal muscles. In vitro experiments indicated that low Pi enhanced and high Pi inhibited insulin signals such as tyrosine phosphorylation of IRβ (Tyr1150/1151) and serine phosphorylation of Akt (Ser473) in primary culture of human skeletal muscle cells (HSkMCs). In addition, low Pi increased and high Pi decreased insulin-induced glucose uptake in HSkMCs. Therefore, these data indicate that low Pi diet regulates glucose homeostasis, partly via enhancing insulin sensitivity through upregulating insulin signals and insulin-induced glucose uptake in skeletal muscles. Disclosure Y. Lin: None. L. Berger: None. Z. Sun: None.
Phenotypic and Genotypic Detection of Extended-Spectrum β-Lactamases (ESBL) among Escherichia coli Isolated from Symptomatic Female's Genital Tract Infection

Clinical E. coli isolates (36) from women (aged 18-45 years) with symptomatic genital tract infection were detected phenotypically and genotypically for ESBL production. Phenotypically, most (30/36: 83.3%) isolates were resistant to cefotaxime (CTX) and more than half of them (26/36: 72.2%) were resistant to ceftazidime (CAZ). All (100%) and 25 (69.4%) of them were ESBLs producers by screening and confirmatory tests, respectively. Genotypically, ESBL genotypes were detected in 31/36 (86.1%) of isolates. All four ESBL genotypes were found among these isolates with predominance of CTX-M-type (26/36: 72.2%) followed by SHV-type (22/36: 61.1%), OXA-type (7/36: 19.4%), and TEM-type (1/36: 2.7%). Of These isolates, 25/36 (69.4%) had two types of ESBL genes. Seventeen (17/22: 77.2%) of SHV-type positive isolates were CTX-M positive. Six (6/7: 85.7%) of OXA-type and the TEM-type positives were also CTX-M- positive whereas the other OXA-type positive isolate was SHV-type positive. Most (22/25: 88%) isolates with two types of ESBLs were resistant to both CTX and CAZ. It can be concluded that, in female's genital tract infection, ESBL production, especially CTX-M-type, can be added as another factor, in addition to virulence factors, that select for certain strains to survive and cause disease and as vaginal E. coli is a reservoir along the fecal-vaginal-urinary/neonatal course of transmission in extraintestinal E. coli infections, our clinicalmicrobiology labs and clinicians need to be aware of the presence of these ESBL-producing organisms and should conduct surveillance studies to ascertain this.
Toxic plants affecting the nervous system of ruminants and horses in Brazil

Riet-Correa F. , Medeiros R.M. T. , Pfister J.A. & Mendonça F.S. 2017. Toxic plants affecting the nervous system of ruminants and horses in Brazil. Pesquisa Veterinária Brasileira 37(12):1357-1368. Laboratório de Diagnóstico Animal, Universidade Federal Rural de Pernambuco, Rua Dom Manoel de Medeiros s/n, Dois Irmãos, Recife, PE 52171-900, Brazil. E-mail: fabio.mendonca@pq.cnpq. br This review updates information about neurotoxic plants affecting ruminants and equidae in Brazil. Currently in the country, there are at least 131 toxic plants belonging to 79 genera. Thirty one of these poisonous plants affect the nervous system. Swainsonine-containing plants (Ipomoea spp., Turbina cordata and Sida carpinifolia) cause numerous outbreaks of poisoning, mainly in goats, but cattle and horses are occasionally affected. The poisoning by Ipomoea asarifolia, a tremorgenic plant, is very common in sheep, goats and cattle in the Northeastern region and in the Marajo island. Poisoning by the pods of Prosopis juliflora are frequent in cattle in Northeastern Brazil; occasionally this poisoning affects goats and more rarely sheep. Some poisonings by plants, such as Hybanthus calceolaria, Ipomoea marcellia and Talisia esculenta in ruminants and Indigofera lespedezioides in horses were recently described and needs to be accurately investigated about its occurrence and importance. Other plants poisonings causing nervous signs in ruminants and equidae are less important, but should be considered for the differential diagnosis of neurologic diseases.
Research paper Lateral line hair cell maturation is a determinant of aminoglycoside susceptibility in zebrafish (Danio rerio)

Developmental differences in hair cell susceptibility to aminoglycoside-induced cell death has been observed in multiple species. Increased sensitivity to aminoglycosides has been temporally correlated with the onset of mechanotransduction-dependent activity. We have used in vivo fluorescent vital dye markers to further investigate the determinants of aminoglycoside induced hair cell death in the lateral line of zebrafish (Danio rerio). Labeling hair cells of the lateral line in vivo with the dyes FM 1-43, To-Pro-3, and YoPro-1 served as reliable indicators of hair cell viability. Results indicate that hair cell maturation is a determinant of developmental differences in susceptibility. The age dependent differences in susceptibility to aminoglycosides are independent of the onset of mechanotransduction-dependent activity as measured by FM 1-43 uptake and independent of hair cell ability to take up fluorescently conjugated aminoglycosides. � 2006 Elsevier B.V. All rights reserved.
Molecular Regulation of Gluconeogenesis by the Nuclear Receptors GR and LXRβ

The long-term use of immunosuppressive glucocorticoid (GC) drugs is limited by undesirable side effects including osteoporosis, obesity, and type 2 diabetes. The potent induction of hepatic glucose production by GCs is known to significantly contribute to the development of type 2 diabetes. Understanding the molecular mediators contributing to the metabolic effects of GCs in the liver will provide a basis from which to generate novel therapeutics to treat this disease. At the cellular level, GCs exert both therapeutic and adverse effects through the activation of the glucocorticoid receptor (GR). Herein, we showed that the gluconeogenic and immune suppressive effects of GC administration can be separated by the liver X receptor β (LXRβ) in mice. Notably, using ChIP assays we demonstrated that either genomic knockdown or antagonism of LXRβ decreases GC-mediated GR recruitment to the GRE of Pepck, a key gluconeogenic gene in mouse liver. This causes decreased expression of Pepck and loss of glucose production following GCiii administration in mouse liver (Chapter 2 and 3). We also demonstrated that LXRβ is dispensable for the GC-mediated immune suppression in mice. Gene expression and glucose production studies in mouse primary macrophages and hepatocytes demonstrated that during GC administration, the beneficial effect of either LXRβ knockdown or LXRβ antagonism is cell autonomous. FGF21 is a hepatokine that regulates whole body insulin sensitivity, and glucose and lipid metabolism. In normal physiology, FGF21 levels are elevated by long term fasting to coordinate the adaptive starvation response (i.e., glucose homeostasis). Using gene expression and ChIP studies we showed that the GC activated-GR directly regulates the starvation hepatokine FGF21 in mouse liver (Chapter 4). In conclusion, we have identified novel modulators that contribute to GC-mediated gluconeogenesis.