Updated List and identification key of 219 tree species of white sand forests of the Allpahuayo Mishana National Reserve, Loreto, Peru

White sand forests, although low in nutrients, are characterized not only by several endemic species of plants but also by several monodominant species. In general, plants in this forest have noticeably thin stems. The aim of this work was to elaborate a parallel dichotomous key for the identification of Angiosperm tree species occurring on white sand forests at the Allpahuayo Mishana National Reserve, Loreto, Peru. We compiled a list of species from several publications in order to have the most comprehensive list of species that occur on white sand forest. We found 219 species of Angiosperm, the more abundant species were Pachira brevipes (26.27%), Caraipa utilis (17.90%), Dicymbe uaiparuensis (13.27%), Dendropanax umbellatus (3.28%), Sloanea spathulata (2.52%), Ternstroemia klugiana (2.30%), Haploclathra cordata (2.28%), Parkia igneiflora (1.20%), Emmotum floribundum (1.06%), Ravenia biramosa (1.04%) among others. Most species of white sand forests can be distinguished using characteristics of stems, branches and leaves. This key is very useful for the development of floristic inventories and related projects on white sand forests from Allpahuayo Mishana National Reserve.

Predicting the distribution of forest tree species using topographic variables and vegetation index in eastern Acre, Brazil

Species distribution modeling has relevant implications for the studies of biodiversity, decision making about conservation and knowledge about ecological requirements of the species. The aim of this study was to evaluate if the use of forest inventories can improve the estimation of occurrence probability, identify the limits of the potential distribution and habitat preference of a group of timber tree species. The environmental predictor variables were: elevation, slope, aspect, normalized difference vegetation index (NDVI) and height above the nearest drainage (HAND). To estimate the distribution of species we used the maximum entropy method (Maxent). In comparison with a random distribution, using topographic variables and vegetation index as features, the Maxent method predicted with an average accuracy of 86% the geographical distribution of studied species. The altitude and NDVI were the most important variables. There were limitations to the interpolation of the models for non-sampled locations and that are outside of the elevation gradient associated with the occurrence data in approximately 7% of the basin area. Ceiba pentandra (samaúma), Castilla ulei (caucho) and Hura crepitans (assacu) is more likely to occur in nearby water course areas. Clarisia racemosa (guariúba), Amburana acreana (cerejeira), Aspidosperma macrocarpon (pereiro), Apuleia leiocarpa (cumaru cetim), Aspidosperma parvifolium (amarelão) and Astronium lecointei (aroeira) can also occur in upland forest and well drained soils. This modeling approach has potential for application on other tropical species still less studied, especially those that are under pressure from logging.

Fine time scaling of purifying selection on human nonsynonymous mtDNA mutations based on the worldwide population tree and mother-child pairs

A high-resolution mtDNA phylogenetic tree allowed us to look backward in time to investigate purifying selection. Purifying selection was very strong in the last 2,500 years, continuously eliminating pathogenic mutations back until the end of the Younger Dryas (∼11,000 years ago), when a large population expansion likely relaxed selection pressure. This was preceded by a phase of stable selection until another relaxation occurred in the out-of-Africa migration. Demography and selection are closely related: expansions led to relaxation of selection and higher pathogenicity mutations significantly decreased the growth of descendants. The only detectible positive selection was the recurrence of highly pathogenic nonsynonymous mutations (m.3394T>C-m.3397A>G-m.3398T>C) at interior branches of the tree, preventing the formation of a dinucleotide STR (TATATA) in the MT-ND1 gene. At the most recent time scale in 124 mother-children transmissions, purifying selection was detectable through the loss of mtDNA variants with high predicted pathogenicity. A few haplogroup-defining sites were also heteroplasmic, agreeing with a significant propensity in 349 positions in the phylogenetic tree to revert back to the ancestral variant. This nonrandom mutation property explains the observation of heteroplasmic mutations at some haplogroup-defining sites in sequencing datasets, which may not indicate poor quality as has been claimed.

A genetic perspective on African prehistory

The various genetic systems (mitochondrial DNA, the Y-chromosome and the genome-wide autosomes) indicate that Africa is the most genetically diverse continent in the world and the most likely place of origin for anatomically modern humans. However, where in Africa modern humans arose and how the current genetic makeup within the continent was shaped is still open to debate. Here, we summarize the debate and focus especially on the maternally inherited mitochondrial DNA (mtDNA) and a recently revised chronology for the African mtDNA tree. We discuss the possible origin of modern humans in southern, eastern or Central Africa; the possibility of a migration from southern to eastern Africa more than 100 ka, carrying lineages within mtDNA haplogroup L0; the evidence for a climate-change-mediated population expansion in eastern Africa involving mtDNA haplogroup L3, leading to the “out-of-Africa” migration around 70–60 ka; the re-population of North Africa from the Near East around 40–30 ka suggested by mtDNA haplogroups U6 and M1; the evidence for population expansions and dispersals across the continent at the onset of the Holocene ; and the impact of the Bantu dispersals in Central, eastern and southern Africa within the last few millennia.

Walking Tree - Organisation neuer Forschung in der Wissenschaft : Zusammenarbeit zwischen Integration und Differenzierung

Magdeburg, Univ., Fak. für Geistes-, Sozial- und Erziehungswiss., Diss., 2011

Habitat use by a tree frog species of Scinax (Amphibia, Hylidae) at an urban forest fragment from south-eastern Brazil

We studied the pattern of habitat use by the tree frog Scinax aff. perereca. Fieldworks were performed from August 1996 to August 1997 at Parque das Mangabeiras, Belo Horizonte, State of Minas Gerais, southeastern Brazil. Calling males were observed in September, October and December 1996, February to April and June 1997. Females were found only in October 1996. Specimens were found perched on vegetation, on the ground or on stones near waterfall. At Parque das Mangabeiras, S. aff. perereca occupied nine types of substrata. The most frequently used substrata were shrubs, stones at the stream edges, and fallen trunks. The pattern of spatial occupation varied among months. Males were found calling in aggregations on the vegetation and spatial niche breadth was related to species abundance.

Use of tree species by White-throated treerunner (Pygarrhichas albogularis King) in a secondary native forest of southern Chile

ABSTRACT In forest ecosystems, numerous species of insectivorous birds use certain tree species as feeding and nesting substrates. Between 2009 and 2010, the use of different floristic components as feeding substrate by the Pygarrhichas albogularis King, 1831 was evaluated in a southern Chilean secondary native forest. From a total of 13 trees and bush species, six tree species were used by P. albogularis as a feeding substrate. Tree use was limited to intermediate heights (11-20 m) and, mainly, to the trunk (40% of observations) and secondary branches (26%). Pygarrhichas albogularis showed a disproportionated use of N. dombeyi and an important use of trees with a greater age structure (DBH 81-100 cm). Nothofagus dombeyi presented a significantly greater tree bark crevice depth than E. cordifolia. In turn, covariance between crevice depth and invertebrate supply in tree bark was positive and significant. We consider bark depth and invertebrate supply to be the proximate causes explaining P. albogularis disproportionated use of Nothofagus dombeyi.

CLOCK-controlled polyphonic regulation of circadian rhythms through canonical and noncanonical E-boxes.

In mammalian circadian clockwork, the CLOCK-BMAL1 complex binds to DNA enhancers of target genes and drives circadian oscillation of transcription. Here we identified 7,978 CLOCK-binding sites in mouse liver by chromatin immunoprecipitation-sequencing (ChIP-Seq), and a newly developed bioinformatics method, motif centrality analysis of ChIP-Seq (MOCCS), revealed a genome-wide distribution of previously unappreciated noncanonical E-boxes targeted by CLOCK. In vitro promoter assays showed that CACGNG, CACGTT, and CATG(T/C)G are functional CLOCK-binding motifs. Furthermore, we extensively revealed rhythmically expressed genes by poly(A)-tailed RNA-Seq and identified 1,629 CLOCK target genes within 11,926 genes expressed in the liver. Our analysis also revealed rhythmically expressed genes that have no apparent CLOCK-binding site, indicating the importance of indirect transcriptional and posttranscriptional regulations. Indirect transcriptional regulation is represented by rhythmic expression of CLOCK-regulated transcription factors, such as Krüppel-like factors (KLFs). Indirect posttranscriptional regulation involves rhythmic microRNAs that were identified by small-RNA-Seq. Collectively, CLOCK-dependent direct transactivation through multiple E-boxes and indirect regulations polyphonically orchestrate dynamic circadian outputs.

Balanceo distribuido del encaminamiento para topologías fat-tree sobre redes Infiniband

Las redes de interconexión juegan un papel importante en el rendimiento de los sistemas de altas prestaciones. Actualmente la gestión del encaminamiento de los mensajes es un factor determinante para mantener las prestaciones de la red. Nuestra propuesta es trabajar sobre un algoritmo de encaminamiento adaptativo, que distribuye el encaminamiento de los mensajes para evitar los problemas de congestión en las redes de interconexión, que aparecen por el gran volumen de comunicaciones de aplicaciones científicas ó comerciales. El objetivo es ajustar el algoritmo a una topología muy utilizada en los sistemas actuales como lo es el fat‐tree, e implementarlo en una tecnología Infiniband. En la experimentación realizada comparamos el método de control de congestión de la arquitectura Infiniband, con nuestro algoritmo. Los resultados obtenidos muestran que mejoramos los niveles de latencia por encima de un 50% y de throughput entre un 38% y un 81%.

Tree automorphisms and quasi-isometries of Thompson's group F

We prove that automorphisms of the infinite binary rooted tree T2 do not yield quasi-isometries of Thompson's group F, except for the map which reverses orientation on the unit interval, a natural outer automorphism of F. This map, together with the identity map, forms a subgroup of Aut(T2) consisting of 2-adic automorphisms, following standard terminology used in the study of branch groups. However, for more general p, we show that the analgous groups of p-adic tree automorphisms do not give rise to quasiisometries of F(p).

In vivo characterization of the circadian clock output gene usp2

Life on earth is subject to the repeated change between day and night periods. All organisms that undergo these alterations have to anticipate consequently the adaptation of their physiology and possess an endogenous periodicity of about 24 hours called circadian rhythm from the Latin circa (about) and diem (day). At the molecular level, virtually all cells of an organism possess a molecular clock which drives rhythmic gene expression and output functions. Besides altered rhythmicity in constant conditions, impaired clock function causes pathophysiological conditions such as diabetes or hypertension. These data unveil a part of the mechanisms underlying the well-described epidemiology of shift work and highlight the function of clock-driven regulatory mechanisms. The post-translational modification of proteins by the ubiquitin polypeptide is a central mechanism to regulate their stability and activity and is capital for clock function. Similarly to the majority of biological processes, it is reversible. Deubiquitylation is carried out by a wide variety of about ninety deubiquitylating enzymes and their function remains poorly understood, especially in vivo. This class of proteolytic enzymes is parted into five families including the Ubiquitin-Specific Proteases (USP), which is the most important with about sixty members. Among them, the Ubiquitin-Specific Protease 2 (Usp2) gene encodes two protein isoforms, USP2-45 and USP2-69. The first is ubiquitously expressed under the control of the circadian clock and displays all features of core clock genes or its closest outputs effectors. Additionally, Usp2-45 was also found to be induced by the mineralocorticoid hormone aldosterone and thought to participate in Na+ reabsorption and blood pressure regulation by Epithelial Na+ Channel ENaC in the kidneys. During my thesis, I aimed to characterize the role of Usp2 in vivo with respect to these two areas, by taking advantage of a total constitutive knockout mouse model. In the first project I aimed to validate the role of USP2-45 in Na+ homeostasis and blood pressure regulation by the kidneys. I found no significant alterations of diurnal Na+ homeostasis and blood pressure in these mice, indicating that Usp2 does not play a substantial role in this process. In urine analyses, we found that our Usp2-KO mice are actually hypercalciuric. In a second project, I aimed to understand the causes of this phenotype. I found that the observed hypercalciuria results essentially from intestinal hyperabsorption. These data reveal a new role for Usp2 as an output effector of the circadian clock in dietary Ca2+ metabolism in the intestine.

Predicting positive food challenges in children sensitised to peanuts/tree nuts.

BACKGROUND: Children with atopic diseases in early life are frequently found with positive IgE tests to peanuts/tree nuts without a history of previous ingestion. We aimed to identify risk factors for reactions to nuts at first introduction. METHODS: A retrospective case-note and database analysis was performed. Recruitment criteria were: patients aged 3-16 yr who had a standardized food challenge to peanut and/or tree nuts due to sensitisation to the peanut/tree nut (positive spIgE or SPT) without previous consumption. A detailed assessment was performed of factors relating to food challenge outcome with univariate and multivariate logistic regression analysis. RESULTS: There were 98 food challenges (47 peanut, 51 tree nut) with 29 positive, 67 negative and 2 inconclusive outcomes. A positive maternal history of allergy and a specific IgE >5 kU/l were strongly associated with a significantly increased risk of a positive food challenge (OR 3.73; 95% CI 1.31-10.59; p = 0.013 and OR 3.35; 95% CI 1.23-9.11; p = 0.007, respectively). Adjusting for age, a three year-old with these criteria has a 67% probability of a positive challenge. There was no significant association between types of peanut/tree nut, other food allergies, atopic conditions or severity of previous food reactions and positive challenges. CONCLUSIONS: We have demonstrated an association between the presence of maternal atopic history and a specific IgE >5 kU/l, with a significant increase in the likelihood of a positive food challenge. Although requiring further prospective validation these easily identifiable components should be considered when deciding the need for a challenge.

A role for clock genes in sleep homeostasis.

The timing and quality of both sleep and wakefulness are thought to be regulated by the interaction of two processes. One of these two processes keeps track of the prior sleep-wake history and controls the homeostatic need for sleep while the other sets the time-of-day that sleep preferably occurs. The molecular pathways underlying the latter, circadian process have been studied in detail and their key role in physiological time-keeping has been well established. Analyses of sleep in mice and flies lacking core circadian clock gene proteins have demonstrated, however, that besides disrupting circadian rhythms, also sleep homeostatic processes were affected. Subsequent studies revealed that sleep loss alters both the mRNA levels and the specific DNA-binding of the key circadian transcriptional regulators to their target sequences in the mouse brain. The fact that sleep loss impinges on the very core of the molecular circadian circuitry might explain why both inadequate sleep and disrupted circadian rhythms can similarly lead to metabolic pathology. The evidence for a role for clock genes in sleep homeostasis will be reviewed here.

Crosstalk between xenobiotics metabolism and circadian clock.

Many aspects of physiology and behavior in organisms from bacteria to man are subjected to circadian regulation. Indeed, the major function of the circadian clock consists in the adaptation of physiology to daily environmental change and the accompanying stresses such as exposition to UV-light and food-contained toxic compounds. In this way, most aspects of xenobiotic detoxification are subjected to circadian regulation. These phenomena are now considered as the molecular basis for the time-dependence of drug toxicities and efficacy. However, there is now evidences that these toxic compounds can, in turn, regulate circadian gene expression and thus influence circadian rhythms. As food seems to be the major regulator of peripheral clock, the possibility that food-contained toxic compounds participate in the entrainment of the clock will be discussed.