Neutral Theory Predicts the Relative Abundance and Diversity of Genetic Elements in a Broad Array of Eukaryotic Genomes

It is universally true in ecological communities, terrestrial or aquatic, temperate or tropical, that some species are very abundant, others are moderately common, and the majority are rare. Likewise, eukaryotic genomes also contain classes or “species” of genetic elements that vary greatly in abundance: DNA transposons, retrotransposons, satellite sequences, simple repeats and their less abundant functional sequences such as RNA or genes. Are the patterns of relative species abundance and diversity similar among ecological communities and genomes? Previous dynamical models of genomic diversity have focused on the selective forces shaping the abundance and diversity of transposable elements (TEs). However, ideally, models of genome dynamics should consider not only TEs, but also the diversity of all genetic classes or “species” populating eukaryotic genomes. Here, in an analysis of the diversity and abundance of genetic elements in >500 eukaryotic chromosomes, we show that the patterns are consistent with a neutral hypothesis of genome assembly in virtually all chromosomes tested. The distributions of relative abundance of genetic elements are quite precisely predicted by the dynamics of an ecological model for which the principle of functional equivalence is the main assumption. We hypothesize that at large temporal scales an overarching neutral or nearly neutral process governs the evolution of abundance and diversity of genetic elements in eukaryotic genomes.     

Modulation of glucan-enzyme interactions by domain V in GTF-SI from Streptococcus mutans

Glucansucrase GTF-SI from Streptococcus mutans is a multidomain enzyme that catalyzes the synthesis of glucan polymers. Domain V locates 100 Å from the catalytic site and is required for an optimal activity. Nevertheless, the mechanism governing its functional role remains elusive. In this work, homology modeling and molecular dynamics simulations were employed to examine the effect of domain V in the structure and glucan-binding ability of GTF-SI in full and truncated enzyme models. Our results showed that domain V increases the flexibility of the α4′-loop-α4″ motif near the catalytic site resulting in a higher surface for glucan association, and modulates the orientation of a growing oligosaccharide (N=8-23) in glucan-enzyme complexes towards engaging in favorable contacts throughout the protein, whereas in the truncated model the glucan protrudes randomly from domain B towards the solvent. These results are valuable to increase understanding about the functional role of domain V in GH70 glucansucrases.     

Population and Genetic Study of Vibrio cholerae from the Amazon Environment Confirms that the WASA-1 Prophage Is the Main Marker of the Epidemic Strain that Circulated in the Region

Vibrio cholerae is a natural inhabitant of many aquatic environments in the world. Biotypes harboring similar virulence-related gene clusters are the causative agents of epidemic cholera, but the majority of strains are harmless to humans. Since 1971, environmental surveillance for potentially pathogenic V. cholerae has resulted in the isolation of many strains from the Brazilian Amazon aquatic ecosystem. Most of these strains are from the non-O1/non-O139 serogroups (NAGs), but toxigenic O1 strains were isolated during the Latin America cholera epidemic in the region (1991-1996). A collection of environmental V. cholerae strains from the Brazilian Amazon belonging to pre-epidemic (1977-1990), epidemic (1991-1996), and post-epidemic (1996-2007) periods in the region, was analyzed. The presence of genes related to virulence within the species and the genetic relationship among the strains were studied. These variables and the information available concerning the strains were used to build a Bayesian multivariate dependency model to distinguish the importance of each variable in determining the others. Some genes related to the epidemic strains were found in environmental NAGs during and after the epidemic. Significant diversity among the virulence-related gene content was observed among O1 strains isolated from the environment during the epidemic period, but not from clinical isolates, which were analyzed as controls. Despite this diversity, these strains exhibited similar PFGE profiles. PFGE profiles were significant while separating potentially epidemic clones from indigenous strains. No significant correlation with isolation source, place or period was observed. The presence of the WASA-1 prophage significantly correlated with serogroups, PFGE profiles, and the presence of virulence-related genes. This study provides a broad characterization of the environmental V. cholerae population from the Amazon, and also highlights the importance of identifying precisely defined genetic markers such as the WASA-1 prophage for the surveillance of cholera.     

The BtaF Trimeric Autotransporter of Brucella suis Is Involved in Attachment to Various Surfaces,Resistance to Serum and Virulence

The adhesion of bacterial pathogens to host cells is an event that determines infection, and ultimately invasion and intracellular multiplication. Several evidences have recently shown that this rule is also truth for the intracellular pathogen Brucella. Brucella suis displays the unipolar BmaC and BtaE adhesins, which belong to the monomeric and trimeric autotransporter (TA) families, respectively. It was previously shown that these adhesins are involved in bacterial adhesion to host cells and components of the extracellular matrix (ECM). In this work we describe the role of a new member of the TA family of B. suis (named BtaF) in the adhesive properties of the bacterial surface. BtaF conferred the bacteria that carried it a promiscuous adhesiveness to various ECM components and the ability to attach to an abiotic surface. Furthermore, BtaF was found to participate in bacterial adhesion to epithelial cells and was required for full virulence in mice. Similar to BmaC and BtaE, the BtaF adhesin was expressed in a small subpopulation of bacteria, and in all cases, it was detected at the new pole generated after cell division. Interestingly, BtaF was also implicated in the resistance of B. suis to porcine serum. Our findings emphasize the impact of TAs in the Brucella lifecycle.     

Pure and mixed plantations of Persian walnut (Juglans regia L.) for high quality timber production in Chile,South America

波斯胡桃(Juglans regia L.)是用于装饰工业的一种森林物种，需要适当的管理才能生产出经济效益好的高质量原木。由于种间关联和管理水平可以提高林分生产力，因此本研究的创新之处在于评估波斯胡桃在不同混合种植中以及在适度的管理强度的纯人工林中的表现。在两种截然不同的管理方案下种植纯林和混交林后，连续7年每年对波斯胡桃的生长、直度和存活率进行测定。在第7年时，记录所有人工林中病害情况。在每种管理强度下，除纯林外，检验三种混交林：仅与主要森林物种混交、主要森林物种和黑桤木(Alnus glutinosa L.，伴生种)混交，以及主要物种和灌木俄罗斯橄榄(Elaeagnus angustifolia L.，保育种)混交。利用重复生长数据对人工林类型与管理方案之间的交互作用进行检验。研究发现人工林类型与管理方案的交互作用显著，表明在管理水平高和低的条件下，人工林效应存在不同的机制。与纯林相比，在低管理水平下，有保育灌木混交的波斯胡桃的树高增加了78%、直径生长增加了53%。同样，在管理强度不高的情况下，与灌木混交有更多的健康益处(胡桃枯萎病的发生率低于单一栽培)和更好的直度。在高管理强度下(灌溉、施肥、抚育和频繁修剪)，与俄罗斯橄榄混交时这些有益效应消失。因此，波斯胡桃种植园的具体选址设计取决于可预见的管理强度。     

Mehler reaction plays a role in C3 and C4 photosynthesis under shade and low CO2

Photosynthesis Research - Alternative electron fluxes such as the cyclic electron flux (CEF) around photosystem I (PSI) and Mehler reaction (Me) are essential for efficient photosynthesis because...     

Extracellular conserved cysteine forms an intersubunit disulphide bridge in the KCNK5 (TASK-2) K + channel without having an essential effect upon activity

The functional channel unit of K + channels with two pore regions in tandem is thought to be a homodimer and it has been suggested that this dimeric structure occurs by interaction of an extracellular domain, the self-interacting domain. Interaction and functional assembly have been studied in some detail for KCNK1. It is proposed that a disulphide bond between highly conserved C69 residues of the self-interacting domain is formed which is essential for channel activity. We mutated C51, the equivalent residue in the pH-dependent KCNK5, to study its effect on channel function. Western analysis of proteins from cells expressing epitope-tagged KCNK5 and KCNK5-C51S was consistent with reduction-sensitive self-association of monomers dependent upon the presence of C51. Patch-clamp analysis of heterologously expressed KCNK5-C51S, however, revealed it was functional and indistinguishable in rectification properties and pH dependence from the non-mutated channel. The same result was found with KCNK5-C115S. It is concluded that the proposed disulphide bond between cysteine 51 residues of KCNK5 subunits does occur and preserves a dimeric structure in the detergent solubilized complex. Functional assays, on the other hand, suggest that such a disulphide bridge is not essential for correct functional expression.     

Multiple refugia and glacial expansions in the Tucumane–Bolivian Yungas: The phylogeography and potential distribution modeling of Calomys fecundus (Thomas, 1926) (Rodentia: Cricetidae)

The Yungas, a subtropical mountain rainforest of South America, has been little studied in relation to the evolutionary history of the large-bodied species of the genus Calomys. Particularly, two species have been synonymized: C. boliviae and C. fecundus; the first is only known from its type locality in the northern Bolivian Yungas, whereas the second is known along the Tucumane–Bolivian Yungas shared by Bolivia and Argentina. In this study, we combined a phylogeographic approach with ecological niche modeling, with samples covering most of the geographic range of C. fecundus. One mitochondrial and two nuclear genes were used for population genetic analyses. Current and paleoclimatic models were obtained. Nuclear genes resulted uninformative by retention of ancestral polymorphism with other species of Calomys. The mitochondrial marker revealed a complex network showing signals of several population expansions. Three genetic clusters in a latitudinal sense were detected, which are coincident with the three stable climatic zones estimated by current and paleoclimatic models. We determined a pattern of expansion during glacial cycles and ancestral refugia during interglacial cycles. None of the potential distribution models predicted the presence of C. fecundus in the type locality of C. boliviae. Therefore, we recommend making integrative taxonomic studies in the Bolivian Yungas, to determine whether or not C. fecundus and C. boliviae correspond to the same species.