The domestic ferret (Mustela putorius furo) is an important animal model for multiple human respiratory diseases. It is considered the 'gold standard' for modeling human influenza virus infection and ...transmission. Here we describe the 2.41 Gb draft genome assembly of the domestic ferret, constituting 2.28 Gb of sequence plus gaps. We annotated 19,910 protein-coding genes on this assembly using RNA-seq data from 21 ferret tissues. We characterized the ferret host response to two influenza virus infections by RNA-seq analysis of 42 ferret samples from influenza time-course data and showed distinct signatures in ferret trachea and lung tissues specific to 1918 or 2009 human pandemic influenza virus infections. Using microarray data from 16 ferret samples reflecting cystic fibrosis disease progression, we showed that transcriptional changes in the CFTR-knockout ferret lung reflect pathways of early disease that cannot be readily studied in human infants with cystic fibrosis disease.
On-site Stormwater Detention has been used around the world to reduce stormwater peak flow at lot scale. However, few studies have evaluated its performance as well as its hydrological and hydraulic ...parameters on a real scale. To evaluate these variables, two OSDs were monitored in Belo Horizonte/Brazil. Based on the analysis of monitoring data, it was observed that: (i) the OSDs average efficiencies in peak flow damping were higher than 50%; (ii) the storage volume per catchment area was close to 25 L/m
2
; (iii) the short tubes discharge coefficients were approximately 0.90 and; (iv) the shape of inflow hydrographs were similar to hyetographs. The use of the Unit Hydrograph Modified Rational Method properly represented the rain-runoff transformation. The findings could be used in OSD design to determine the inlet hydrograph, to pre-sizing the storage volume based on contribution area and to use the proper discharge coefficient value for outlet device.
In recent decades On-site Stormwater Detention (OSD) systems have been implemented in many cities around the world. However, a few studies have evaluated the effectiveness of OSD policies. Therefore, ...this paper compared the use of OSD in Australian and Brazilian cities, evaluating aspects of regulations, technical details and management matters. The results showed that Australian OSD design guidelines are a few steps ahead of Brazilian manuals. However, it is not possible to affirm that the catchment-based approach, adopted by most Australian councils, is better than the site-based approach, embraced by Brazilian cities, since neither is supported by monitoring data of real OSD performance. In general, all municipalities have the same management problems. There is no control over the number of OSDs built in the cities or even the conditions of the systems. Thus, the authors proposed some directions on how OSD policies could be improved.
To connect human biology to fish biomedical models, we sequenced the genome of spotted gar (Lepisosteus oculatus), whose lineage diverged from teleosts before teleost genome duplication (TGD). The ...slowly evolving gar genome has conserved in content and size many entire chromosomes from bony vertebrate ancestors. Gar bridges teleosts to tetrapods by illuminating the evolution of immunity, mineralization and development (mediated, for example, by Hox, ParaHox and microRNA genes). Numerous conserved noncoding elements (CNEs; often cis regulatory) undetectable in direct human-teleost comparisons become apparent using gar: functional studies uncovered conserved roles for such cryptic CNEs, facilitating annotation of sequences identified in human genome-wide association studies. Transcriptomic analyses showed that the sums of expression domains and expression levels for duplicated teleost genes often approximate the patterns and levels of expression for gar genes, consistent with subfunctionalization. The gar genome provides a resource for understanding evolution after genome duplication, the origin of vertebrate genomes and the function of human regulatory sequences.
Cichlid fishes are famous for large, diverse and replicated adaptive radiations in the Great Lakes of East Africa. To understand the molecular mechanisms underlying cichlid phenotypic diversity, we ...sequenced the genomes and transcriptomes of five lineages of African cichlids: the Nile tilapia (Oreochromis niloticus), an ancestral lineage with low diversity; and four members of the East African lineage: Neolamprologus brichardi/pulcher (older radiation, Lake Tanganyika), Metriaclima zebra (recent radiation, Lake Malawi), Pundamilia nyererei (very recent radiation, Lake Victoria), and Astatotilapia burtoni (riverine species around Lake Tanganyika). We found an excess of gene duplications in the East African lineage compared to tilapia and other teleosts, an abundance of non-coding element divergence, accelerated coding sequence evolution, expression divergence associated with transposable element insertions, and regulation by novel microRNAs. In addition, we analysed sequence data from sixty individuals representing six closely related species from Lake Victoria, and show genome-wide diversifying selection on coding and regulatory variants, some of which were recruited from ancient polymorphisms. We conclude that a number of molecular mechanisms shaped East African cichlid genomes, and that amassing of standing variation during periods of relaxed purifying selection may have been important in facilitating subsequent evolutionary diversification.
Celotno besedilo
Dostopno za:
DOBA, IJS, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
We present evidence that a relatively widespread and common bat from South East Asia comprises two morphologically cryptic but acoustically divergent species. A population of the bicoloured ...leaf-nosed bat (Hipposideros bicolor) from Peninsular Malaysia exhibits a bimodal distribution of echolocation call frequencies, with peaks in the frequency of maximum energy at ca. 131 and 142 kHz. The two phonic types are genetically distinct, with a cytochrome b sequence divergence of just under 7%. We consider the mechanisms by which acoustic divergence in these species might arise. Differences in call frequency are not likely to effect resource partitioning by detectable prey size or functional range. However, ecological segregation may be achieved by differences in microhabitat use; the 131 kHz H. bicolor is characterized by significantly longer forearms, lower wing loading, a lower aspect ratio and a more rounded wingtip, features that are associated with greater manoeuvrability in flight that may enable it to forage in more cluttered environments relative to the 142 kHz phonic type. We suggest that acoustic divergence in these species is a consequence of social selection for a clear communication channel, which is mediated by the close link between the acoustic signal and receptor systems imposed by the highly specialized nature of the hipposiderid and rhinolophid echolocation system.
An experimentally study of water level changes at open channel junctions with angles of 30° and 60° for different flow conditions is presented. The experimental results were used to assess the equal ...water level assumption commonly adopted in confluence studies. The maximum value of the water depth at the confluence was assessed through comparison with the critical depth in the downstream channel. Additionally, the results were used to validate the generalization of a classical model for estimating the water depth in confluences with subcritical flows downstream from the junction, even in cases where one or both upstream channel flows were supercritical. The maximum average deviations between the model predictions and measurements were approximately 6%.
Hypostomus
shows wide morphological patterns, corroborated by great chromosomal diversity that has suggested the existence of new species, especially from small tributaries. Cytogenetic analysis has ...contributed to estimate a cryptic diversity providing important data for taxonomic and evolutionary studies. Cytogenetic techniques were carried out on species from a small tributary of Ivaí River, Keller River (upper Paraná River basin):
Hypostomus
aff.
ancistroides
,
Hypostomus topavae
, and
Hypostomus
aff.
hermanni
that presented 2n = 68, 80, and 72 chromosomes, respectively. Each species showed the same diploid number from previous descriptions for other populations but different karyotype formulas, and
Hypostomus
aff.
ancistroides
had a ZZ/ZW sex chromosome system. Multiple NORs (nucleolar organizer regions) and pericentromeric heterochromatin blocks were found in the three species. Moreover, each of them showed species-specific heterochromatins. Multiple 5S rDNA sites were detected in
Hypostomus
aff.
ancistroides
and
H
.
topavae
, whereas
Hypostomus
aff.
hermanni
had only one pair bearing these sites. In addition to the divergence in the karyotype formulas, chromosomal markers used showed karyotype differences in the three species related to other respective populations studied. Furthermore, the first description of a ZZ/ZW system for
Hypostomus
aff.
ancistroides
reinforces the hypothesis that it may correspond to a species complex and yet, confirming an unknown cryptic diversity existent in small rivers.
The comparison of related genomes has emerged as a powerful lens for genome interpretation. Here we report the sequencing and comparative analysis of 29 eutherian genomes. We confirm that at least ...5.5% of the human genome has undergone purifying selection, and locate constrained elements covering ∼4.2% of the genome. We use evolutionary signatures and comparisons with experimental data sets to suggest candidate functions for ∼60% of constrained bases. These elements reveal a small number of new coding exons, candidate stop codon readthrough events and over 10,000 regions of overlapping synonymous constraint within protein-coding exons. We find 220 candidate RNA structural families, and nearly a million elements overlapping potential promoter, enhancer and insulator regions. We report specific amino acid residues that have undergone positive selection, 280,000 non-coding elements exapted from mobile elements and more than 1,000 primate- and human-accelerated elements. Overlap with disease-associated variants indicates that our findings will be relevant for studies of human biology, health and disease.
Celotno besedilo
Dostopno za:
DOBA, IJS, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
The evolution of the amniotic egg was one of the great evolutionary innovations in the history of life, freeing vertebrates from an obligatory connection to water and thus permitting the conquest of ...terrestrial environments. Among amniotes, genome sequences are available for mammals and birds, but not for non-avian reptiles. Here we report the genome sequence of the North American green anole lizard, Anolis carolinensis. We find that A. carolinensis microchromosomes are highly syntenic with chicken microchromosomes, yet do not exhibit the high GC and low repeat content that are characteristic of avian microchromosomes. Also, A. carolinensis mobile elements are very young and diverse-more so than in any other sequenced amniote genome. The GC content of this lizard genome is also unusual in its homogeneity, unlike the regionally variable GC content found in mammals and birds. We describe and assign sequence to the previously unknown A. carolinensis X chromosome. Comparative gene analysis shows that amniote egg proteins have evolved significantly more rapidly than other proteins. An anole phylogeny resolves basal branches to illuminate the history of their repeated adaptive radiations.
Celotno besedilo
Dostopno za:
DOBA, IJS, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
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