Gas Accretion and Star Formation Rates

Cosmological numerical simulations of galaxy evolution show that accretion of metal-poor gas from the cosmic web drives the star formation in galaxy disks. Unfortunately, the observational support for this theoretical prediction is still indirect, and modeling and analysis are required to identify hints as actual signs of star-formation feeding from metal-poor gas accretion. Thus, a meticulous interpretation of the observations is crucial, and this observational review begins with a simple theoretical description of the physical process and the key ingredients it involves, including the properties of the accreted gas and of the star-formation that it induces. A number of observations pointing out the connection between metal-poor gas accretion and star-formation are analyzed, specifically, the short gas consumption time-scale compared to the age of the stellar populations, the fundamental metallicity relationship, the relationship between disk morphology and gas metallicity, the existence of metallicity drops in starbursts of star-forming galaxies, the so-called G dwarf problem, the existence of a minimum metallicity for the star-forming gas in the local universe, the origin of the alpha-enhanced gas forming stars in the local universe, the metallicity of the quiescent BCDs, and the direct measurements of gas accretion onto galaxies. A final section discusses intrinsic difficulties to obtain direct observational evidence, and points out alternative observational pathways to further consolidate the current ideas.Comment: Invited review to appear in Gas Accretion onto Galaxies, Astrophysics and Space Science Library, eds. A. J. Fox & R. Dav\'e, to be published by Springe

Guidelines for the use and interpretation of assays for monitoring autophagy (3rd edition)

In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. For example, a key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process versus those that measure fl ux through the autophagy pathway (i.e., the complete process including the amount and rate of cargo sequestered and degraded). In particular, a block in macroautophagy that results in autophagosome accumulation must be differentiated from stimuli that increase autophagic activity, defi ned as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (inmost higher eukaryotes and some protists such as Dictyostelium ) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the fi eld understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. It is worth emphasizing here that lysosomal digestion is a stage of autophagy and evaluating its competence is a crucial part of the evaluation of autophagic flux, or complete autophagy. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. Along these lines, because of the potential for pleiotropic effects due to blocking autophagy through genetic manipulation it is imperative to delete or knock down more than one autophagy-related gene. In addition, some individual Atg proteins, or groups of proteins, are involved in other cellular pathways so not all Atg proteins can be used as a specific marker for an autophagic process. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field

Identification and Characterization of Highly Divergent Simian Foamy Viruses in a Wide Range of New World Primates from Brazil

<div><p>Foamy viruses naturally infect a wide range of mammals, including Old World (OWP) and New World primates (NWP), which are collectively called simian foamy viruses (SFV). While NWP species in Central and South America are highly diverse, only SFV from captive marmoset, spider monkey, and squirrel monkey have been genetically characterized and the molecular epidemiology of SFV infection in NWPs remains unknown. We tested a large collection of genomic DNA (n  = 332) comprising 14 genera of NWP species for the presence of SFV polymerase (<i>pol</i>) sequences using generic PCR primers. Further molecular characterization of positive samples was carried out by LTR-<i>gag</i> and larger <i>pol</i> sequence analysis. We identified novel SFVs infecting nine NWP genera. Prevalence rates varied between 14–30% in different species for which at least 10 specimens were tested. High SFV genetic diversity among NWP up to 50% in LTR-<i>gag</i> and 40% in <i>pol</i> was revealed by intragenus and intrafamilial comparisons. Two different SFV strains infecting two captive yellow-breasted capuchins did not group in species-specific lineages but rather clustered with SFVs from marmoset and spider monkeys, indicating independent cross-species transmission events. We describe the first SFV epidemiology study of NWP, and the first evidence of SFV infection in wild NWPs. We also document a wide distribution of distinct SFVs in 14 NWP genera, including two novel co-speciating SFVs in capuchins and howler monkeys, suggestive of an ancient evolutionary history in NWPs for at least 28 million years. A high SFV genetic diversity was seen among NWP, yet these viruses seem able to jump between NWP species and even genera. Our results raise concerns for the risk of zoonotic transmission of NWP SFV to humans as these primates are regularly hunted for food or kept as pets in forest regions of South America.</p></div

Geographic distribution of distinct <i>Cebus</i> (<i>A</i>), <i>Ateles</i> (<i>B</i>) and <i>Alouatta</i> (<i>C</i>) primate species in Brazil.

<p>Data are according to the Database of Georeferenced Occurrence Localities of Neotropical Primates, Department of Zoology, Universidade Federal de Minas Gerais, Brazil (<a href="http://www.icb.ufmg.br/zoo/primatas/home_bdgeoprim.htm" target="_blank">http://www.icb.ufmg.br/zoo/primatas/home_bdgeoprim.htm</a>). Primate center and wild animal site locations within Brazil (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0067568#pone-0067568-t004" target="_blank">Table 4</a>) are shown: Pará (PA), Mato Grosso (MT), Rondônia (RO), Paraíba (PB), and Brazil/Argentina frontier (RS).</p

Molecular detection and distribution of SFV in New World primates from Brazil.

a<p>NWP common names are as in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0067568#pone.0067568-Groves1" target="_blank">[19]</a>.</p>b<p>PCR testing using diagnostic primers to detect 192-bp polymerase sequences in DNA specimens from species listed.</p>c<p>Underlined numbers refer to specimens from the wild.</p

Time to most recent common ancestor (tMRCA) mean estimates for Haplorrhini and simian foamy virus (SFV) polymerase (<i>pol)</i> and simian cytochrome B (<i>cytB</i>) sequences^a.

a<p>Using an alignment of 276-bp of 1^st and 2^nd codon positions for 18 SFV taxa and 500-bp of all codon positions for 31 <i>cytB</i> taxa. Million years (MY) ago. Geometric means inferred using Bayesian methods and a relaxed clock; ranges in parentheses are 95% highest posterior density intervals.</p>b<p>Dating and fossil estimates from Perelman <i>et al.</i> 2011 <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0067568#pone.0067568-Perelman1" target="_blank">[30]</a>.</p>c<p>ND, not determined.</p>d<p>NA, not available.</p

SFV PCR prevalence in NWP living at primate centers and in the wild^a.

a<p>PCR testing using diagnostic primers to detect 192-bp polymerase sequences in DNA specimens from species listed;</p>b<p>UHE, Usina Hidroelétrica; CNP, Centro Nacional de Primatologia; CPB, Centro de Proteção de Primatas Brasileiros, Instituto Chico Mendes de Conservação da Biodiversidade; CEMIC, Centro de Educación Médica e Investigaciones Clínicas Norberto Quirno;</p>c<p>N, north; SE, southeast; NE, northeast; S, south.</p

Figure 5

<p>Correlation of (<i>A</i>) branch lengths (substitutions per site) and (<i>B</i>) coalescence times (genetic distances) of primate cytochrome B and SFV polymerase (<i>pol</i>) Bayesian-inferred phylogenetic trees.</p

Identification of broad simian foamy virus (SFV) diversity in New World primates (NWPs).

<p>Phylogenetic inference of 265-bp SFV long terminal repeat (LTR)/<i>gag</i> (<i>A</i>) and 276-bp polymerase (<i>pol)</i> (<i>B</i>) sequences from neotropical primate species. SFV sequences retrieved from GenBank are shown with their respective accession numbers, while the remaining SFV are those generated in the study. The newly characterized SFV lineages infecting capuchins (SFVcap) and howler monkeys (SFVhow) can be seen in both panels. Scale bar for the SFV LTR/<i>gag</i> tree is in nucleotide substitutions per site. Statistical support for branch nodes in the LTR/<i>gag</i> tree are provided as bootstrap values from neighbor-joining (NJ) and maximum likelihood (ML) methods and posterior probabilities from Bayesian inference (BI) in the order NJ/ML/BI. # indicates statistical support was not provided by the respective program. Topology and divergence dates for the <i>pol</i> tree were inferred using a relaxed molecular clock and a Yule tree prior using BEAST v1.6.2. X axis is in millions of years. Posterior probabilities >0.8 are provided at nodes.</p