Evolutionary origins of genomic repertoires in bacteria

Explaining the diversity of gene repertoires has been a major problem in modern evolutionary biology. In eukaryotes, this diversity is believed to result mainly from gene duplication and loss, but in prokaryotes, lateral gene transfer (LGT) can also contribute substantially to genome contents. To determine the histories of gene inventories, we conducted an exhaustive analysis of gene phylogenies for all gene families in a widely sampled group, the γ-Proteobacteria. We show that, although these bacterial genomes display striking differences in gene repertoires, most gene families having representatives in several species have congruent histories. Other than the few vast multigene families, gene duplication has contributed relatively little to the contents of these genomes; instead, LGT, over time, provides most of the diversity in genomic repertoires. Most such acquired genes are lost, but the majority of those that persist in genomes are transmitted strictly vertically. Although our analyses are limited to the γ-Proteobacteria, these results resolve a long-standing paradox—i.e., the ability to make robust phylogenetic inferences in light of substantial LGT.     

Energy drives the dynamic localization of cyanobacterial nitrogen regulators during diurnal cycles

Cyanobacteria, phototrophic organisms performing oxygenic photosynthesis, must adapt their metabolic processes to the challenges imposed by the succession of days and nights. Two conserved cyanobacterial proteins, PII and PipX, function as hubs of the nitrogen interaction network, forming complexes with a variety of diverse targets. While PII proteins are found in all three domains of life as integrators of signals of the nitrogen and carbon balance, PipX proteins are unique to cyanobacteria, where they provide a mechanistic link between PII signalling and the control of gene expression by the global nitrogen regulator NtcA. Here we demonstrate that PII and PipX display distinct localization patterns during diurnal cycles, co‐localizing into the same foci at the periphery and poles of the cells during dark periods, a circadian‐independent process requiring a low ATP/ADP ratio. Genetic, cellular biology and biochemical approaches used here provide new insights into the nitrogen regulatory network, calling attention to the roles of PII as energy sensors and its interactions with PipX in the context of essential signalling pathways. This study expands the contribution of the nitrogen regulators PII and PipX to integrate and transduce key environmental signals that allow cyanobacteria to thrive in our planet.     

A geography‐aware reconciliation method to investigate diversification patterns in host/parasite interactions

Cospeciation studies aim at investigating whether hosts and symbionts speciate simultaneously or whether the associations diversify through host shifts. This problem is often tackled through reconciliation analyses that map the symbiont phylogeny onto the host phylogeny by mixing different types of diversification events. These reconciliations can be difficult to interpret and are not always biologically realistic. Researchers have underlined that the biogeographic histories of both hosts and symbionts influence the probability of cospeciation and host switches, but up to now no reconciliation software integrates geographic data. We present a new functionality in the Mowgli software that bridges this gap. The user can provide geographic information on both the host and symbiont extant and ancestral taxa. Constraints in the reconciliation algorithm have been implemented to generate biologically realistic codiversification scenarios. We apply our method to the fig/fig wasp association and infer diversification scenarios that differ from reconciliations ignoring geographic information. In addition, we updated the reconciliation viewer SylvX to visualize ancestral character states on the phylogenetic trees and highlight parts of reconciliations that are geographically inconsistent when not accounting for geographic constraints. We suggest that the comparison of reconciliations obtained with and without such constraints can help solving ambiguities in the biogeographic histories of the partners. With the development of robust methods in historical biogeography, and the advent of next‐generation sequencing that leads to better‐resolved trees, a geography‐aware reconciliation method represents a substantial advance that is likely to be useful to researchers studying the evolution of biotic interactions and biogeography.     

Whole-exon sequencing of human myeloma cell lines shows mutations related to myeloma patients at relapse with major hits in the DNA regulation and repair pathways

Background

Human myeloma cell lines (HMCLs) are widely used for their representation of primary myeloma cells because they cover patient diversity, although not fully. Their genetic background is mostly undiscovered, and no comprehensive study has ever been conducted in order to reveal those details.

Methods

We performed whole-exon sequencing of 33 HMCLs, which were established over the last 50?years in 12 laboratories. Gene expression profiling and drug testing for the 33 HMCLs are also provided and correlated to exon-sequencing findings.

Results

Missense mutations were the most frequent hits in genes (92%). HMCLs harbored between 307 and 916 mutations per sample, with TP53 being the most mutated gene (67%). Recurrent bi-allelic losses were found in genes involved in cell cycle regulation (RB1, CDKN2C), the NFκB pathway (TRAF3, BIRC2), and the p53 pathway (TP53, CDKN2A). Frequency of mutations/deletions in HMCLs were either similar to that of patients (e.g., DIS3, PRDM1, KRAS) or highly increased (e.g., TP53, CDKN2C, NRAS, PRKD2). MAPK was the most altered pathway (82% of HMCLs), mainly by RAS mutants. Surprisingly, HMCLs displayed alterations in epigenetic (73%) and Fanconi anemia (54%) and few alterations in apoptotic machinery. We further identified mutually exclusive and associated mutations/deletions in genes involved in the MAPK and p53 pathways as well as in chromatin regulator/modifier genes. Finally, by combining the gene expression profile, gene mutation, gene deletion, and drug response, we demonstrated that several targeted drugs overcome or bypass some mutations.

Conclusions

With this work, we retrieved genomic alterations of HMCLs, highlighting that they display numerous and unprecedented abnormalities, especially in DNA regulation and repair pathways. Furthermore, we demonstrate that HMCLs are a reliable model for drug screening for refractory patients at diagnosis or at relapse.

     

Personality and performance are affected by age and early life parameters in a small primate

A whole suite of parameters is likely to influence the behavior and performance of individuals as adults, including correlations between phenotypic traits or an individual's developmental context. Here, we ask the question whether behavior and physical performance traits are correlated and how early life parameters such as birth weight, litter size, and growth can influence these traits as measured during adulthood. We studied 486 captive gray mouse lemurs (Microcebus murinus) and measured two behavioral traits and two performance traits potentially involved in two functions: exploration behavior with pull strength and agitation score with bite force. We checked for the existence of behavioral consistency in behaviors and explored correlations between behavior, performance, morphology. We analyzed the effect of birth weight, growth, and litter size, while controlling for age, sex, and body weight. Behavior and performance were not correlated with one another, but were both influenced by age. Growth rate had a positive effect on adult morphology, and birth weight significantly affected emergence latency and bite force. Grip strength was not directly affected by early life traits, but bite performance and exploration behavior were impacted by birth weight. This study shows how early life parameters impact personality and performance.     

Effect of some electron donors and acceptors on redox capacity and simultaneous net H+/K+ fluxes by aeroponic sunflower seedling roots: Evidence for a CN−-resistant redox chain accessible to nonpermeative redox compounds

Summary Excised roots from aeroponic axenically 48 h dark-grown sunflower (Helianthus annuus L.) seedlings showed redox activities, being able to oxidize/reduce all the exogenously added electron donors/acceptors, that affected the H⁺/K⁺ net fluxes simultaneously measured in the medium. Trials were performed with in vivo and CN^–-poisoned roots; these showed null⁺/K⁺ net flux activity but still oxidized/reduced all the e^– donors/acceptors tested except NADH. NADH enhanced the rate of H⁺ efflux by in vivo roots, otherwise not changing any of the normal flux kinetic characteristics, suggesting that NADH donates e^– and H⁺ to the exocellular NADH oxidoreductase activity of a CN^–-sensitive redox chain in the plasmalemma of the root cells. K⁺ influx was not affected, probably because the NADH concentration was not very high. The e^– donor HFC(hexacyanoferrate)(II) activated the H⁺ efflux in a very different way: maximum H⁺ efflux rate was maintained, but both the maximum rate plateau and the optimal pH range were extended, and hence the total H⁺ efflux was significantly enhanced. At the same time, the K⁺ influx was doubled. The different H⁺-efflux kinetics, together with the small but significant HCF(II) oxidation by CN^–-poisoned roots, were taken as evidence that, besides the CN^–-sensitive redox chain, an alternative CN^–-resistant redox chain in the plasmalemma was involved in HCF(II) oxidation. The effect of the oxidized form HCF(III) on H⁺ and K⁺ fluxes was the opposite to that described for HCF(II), but the other H⁺ efflux kinetic characteristics were similar (the maximum rate plateau was extended so that total H⁺ efflux equaled that of the controls). It is proposed that HCF(III) accepts e^– only from the alternative CN^–-resistant redox chain. We could not measure the effect of HCI(hexachloroiridate)(IV) on H+ efflux, as the pH electrodes alone quickly reduced the compound. HCI(IV) promoted a rapid transitory K⁺ efflux, followed by recovery of K⁺ influx. The HCI(IV) reduction by in vivo or CN^–-poisoned roots was extremely rapid, following similar kinetics. Thus, only the CN^–-resistant redox chain was involved in both cases. The redox chain inhibitor cis-platinum(II) annulled ion fluxes in the presence of both NADH and HCF(III), and later even inverted them (a small H⁺ influx down the gradient would induce K⁺ efflux). Cis-platinum(II) did not affect HCF(III) reduction by in vivo roots, and only slightly depressed that by CN^–-poisoned roots. Overall, the effects of the exogenously added e^– donors/acceptors tested were consistent with the existence of a CN^–-resistant redox chain in the plasmalemma of the root cells which would donate/accept e^– even when the H⁺ and K⁺ fluxes were annulled by CN^– or even inverted by cis-platinum(II) treatments. Thus, in the plasmalemma of in vivo roots this chain would compete for electrons with the normal CN^–-sensitive one, as in plant mitochondria. The effects on the K⁺ flux were consistent with the current hypothesis that this contributes to counteracting the changes in membrane potential caused by redox activities and the H⁺ flux induced by the different redox compounds tested.Abbreviations cis-Pt(II) cis-platinum(II) diammine dichloride - HCF(II) hexacyanoferrate(II) (or ferrocyanide) potassium salt - HCF(III) hexacyanoferrate(III) (or ferricyanide) potassium salt - HCI(IV) hexachloroiridate(IV) - PMOR plasmalemma oxidoreductase complex     

Effect of mare's age and recovery methods on the recovery rate of equine follicular oocytes for IVM procedures

Mares (n = 39) were classified according to age as young (less than 1.5 yr, n = 17) or old (more than 1.5 yr, n = 22) and sacrificed. Ovaries were measured and weighed, and the number of follicles and CL were counted. Follicle size and distribution were recorded (external: > 20 mm, < 20 mm; internal: > 5 mm, < 5 mm). External follicles were aspirated while internal follicles were sliced. The number and Type of oocytes recovered using each method were recorded. Oocyte recovery rates (oocytes/ovary) resulted in a mean of 0.92 oocytes by aspiration and 1.36 oocytes by additional slicing. The mean numbers of available follicles (8.11 and 5.02) oocytes recovered (4.94 and 3.02) and oocytes selected per ovary (3.29 and 2.32) were not significantly different in the young or old mares, respectively.