An inter‐species protein–protein interaction network across vast evolutionary distance

In cellular systems, biophysical interactions between macromolecules underlie a complex web of functional interactions. How biophysical and functional networks are coordinated, whether all biophysical interactions correspond to functional interactions, and how such biophysical‐versus‐functional network coordination is shaped by evolutionary forces are all largely unanswered questions. Here, we investigate these questions using an “inter‐interactome” approach. We systematically probed the yeast and human proteomes for interactions between proteins from these two species and functionally characterized the resulting inter‐interactome network. After a billion years of evolutionary divergence, the yeast and human proteomes are still capable of forming a biophysical network with properties that resemble those of intra‐species networks. Although substantially reduced relative to intra‐species networks, the levels of functional overlap in the yeast–human inter‐interactome network uncover significant remnants of co‐functionality widely preserved in the two proteomes beyond human–yeast homologs. Our data support evolutionary selection against biophysical interactions between proteins with little or no co‐functionality. Such non‐functional interactions, however, represent a reservoir from which nascent functional interactions may arise.     

Integrated Analysis of Environment,Cattle and Human Serological Data: Risks and Mechanisms of Transmission of Rift Valley Fever in Madagascar

BackgroundRift Valley fever (RVF) is a vector-borne disease affecting ruminants and humans. Madagascar was heavily affected by RVF in 2008–2009, with evidence of a large and heterogeneous spread of the disease. The identification of at-risk environments is essential to optimize the available resources by targeting RVF surveillance in Madagascar. Herein, the objectives of our study were: (i) to identify the environmental factors and areas favorable to RVF transmission to both cattle and human and (ii) to identify human behaviors favoring human infections in Malagasy contexts.Conclusions/SignificanceOur integrated approach analyzing environmental, cattle and human datasets allow us to bring new insight on RVF transmission patterns in Madagascar. The association between cattle seroprevalence, humid environments and high cattle density suggests that concomitant vectorial and direct transmissions are critical to maintain RVF enzootic transmission. Additionally, in the at-risk humid environment of the western, north-western and the eastern-coast areas, suitable to Culex and Anopheles mosquitoes, vectorial transmission probably occurs in both cattle and human. The relative contribution of vectorial or direct transmissions could be further assessed by mathematic modelling.     

Enhancement of embryo yield from isolated microspores of <Emphasis Type="Italic">Brassica napus</Emphasis> by early iron starvation

Induction of embryogenesis in isolated microspores of Brassica napus requires stress conditions to trigger the developmental instead of the gametophytic pathway. To obtain further insight into the involvement of different ions in this process, a comparison has been made between embryo yields obtained with standard NLN-13 medium and the same medium without cobalt, copper or iron. It was confirmed that iron was essential to control embryo development, but not cobalt and copper. For the latter two ions, the concentration is probably too low to play a significant role in microspore embryogenesis. With the timing of iron application, as well as its chemical form, embryo yield could be improved or reduced. In media that exhibited iron deficiency, microspores initiated embryogenesis and the number of observed divided microspores increased 6 days after isolation. However, embryo development was not achieved. Addition of iron ions chelated with EDTA at day 3, leading to the doubling of embryo yield. Some of the putative role(s) of Fe-EDTA in the early events of embryogenesis is discussed.     

Non-Invasive Monitoring of Temporal and Spatial Blood Flow during Bone Graft Healing Using Diffuse Correlation Spectroscopy

Vascular infiltration and associated alterations in microvascular blood flow are critical for complete bone graft healing. Therefore, real-time, longitudinal measurement of blood flow has the potential to successfully predict graft healing outcomes. Herein, we non-invasively measure longitudinal blood flow changes in bone autografts and allografts using diffuse correlation spectroscopy in a murine femoral segmental defect model. Blood flow was measured at several positions proximal and distal to the graft site before implantation and every week post-implantation for a total of 9 weeks (autograft n = 7 and allograft n = 10). Measurements of the ipsilateral leg with the graft were compared with those of the intact contralateral control leg. Both autografts and allografts exhibited an initial increase in blood flow followed by a gradual return to baseline levels. Blood flow elevation lasted up to 2 weeks in autografts, but this duration varied from 2 to 6 weeks in allografts depending on the spatial location of the measurement. Intact contralateral control leg blood flow remained at baseline levels throughout the 9 weeks in the autograft group; however, in the allograft group, blood flow followed a similar trend to the graft leg. Blood flow difference between the graft and contralateral legs (ΔrBF), a parameter defined to estimate graft-specific changes, was elevated at 1–2 weeks for the autograft group, and at 2–4 weeks for the allograft group at the proximal and the central locations. However, distal to the graft, the allograft group exhibited significantly greater ΔrBF than the autograft group at 3 weeks post-surgery (p < 0.05). These spatial and temporal differences in blood flow supports established trends of delayed healing in allografts versus autografts.     

Hepatitis B virus Core protein nuclear interactome identifies SRSF10 as a host RNA-binding protein restricting HBV RNA production

Despite the existence of a preventive vaccine, chronic infection with Hepatitis B virus (HBV) affects more than 250 million people and represents a major global cause of hepatocellular carcinoma (HCC) worldwide. Current clinical treatments, in most of cases, do not eliminate viral genome that persists as a DNA episome in the nucleus of hepatocytes and constitutes a stable template for the continuous expression of viral genes. Several studies suggest that, among viral factors, the HBV core protein (HBc), well-known for its structural role in the cytoplasm, could have critical regulatory functions in the nucleus of infected hepatocytes. To elucidate these functions, we performed a proteomic analysis of HBc-interacting host-factors in the nucleus of differentiated HepaRG, a surrogate model of human hepatocytes. The HBc interactome was found to consist primarily of RNA-binding proteins (RBPs), which are involved in various aspects of mRNA metabolism. Among them, we focused our studies on SRSF10, a RBP that was previously shown to regulate alternative splicing (AS) in a phosphorylation-dependent manner and to control stress and DNA damage responses, as well as viral replication. Functional studies combining SRSF10 knockdown and a pharmacological inhibitor of SRSF10 phosphorylation (1C8) showed that SRSF10 behaves as a restriction factor that regulates HBV RNAs levels and that its dephosphorylated form is likely responsible for the anti-viral effect. Surprisingly, neither SRSF10 knock-down nor 1C8 treatment modified the splicing of HBV RNAs but rather modulated the level of nascent HBV RNA. Altogether, our work suggests that in the nucleus of infected cells HBc interacts with multiple RBPs that regulate viral RNA metabolism. Our identification of SRSF10 as a new anti-HBV restriction factor offers new perspectives for the development of new host-targeted antiviral strategies.     

Molecular analysis of methanogenic archaea in the forestomach of the alpaca (Vicugna pacos)

Background  

Methanogens that populate the gastrointestinal tract of livestock ruminants contribute significantly to methane emissions from the agriculture industry. There is a great need to analyze archaeal microbiomes from a broad range of host species in order to establish causal relationships between the structure of methanogen communities and their potential for methane emission. In this report, we present an investigation of methanogenic archaeal populations in the foregut of alpacas.     

A comparison of mean weights and the variability of weights of twelve bilateral muscles of the Japanese quail (Coturnix c. japonica) studied in four generations of consanguine crosses]

The influence of the increase of the degree of homozygosity, obtained by successive consanguine cross-breeding, on the mean weights and the variability of the weights of twelve muscles of the Japanese quail (Coturnix c. japonica) was studied in four generations of females and two generations of males. It was found that the mean weights of the twelve muscles in both sexes showed a progressive reduction in the consecutive generations of consanguine crosses, this reduction being more marked in the males than in the females. These results support the hypotheses of Haldane and Lerner that heterozygotes are at an advantage, having a more active metabolism and a greater rate of growth, because their richer biochemical system and greater number of alleles coding the enzymes enables them to benefit from their environment to a greater extent and within wider limits. The rates of decrease vary from one muscle to the other within the limits of 5.3 and 16.6%. For certain muscles there are also notable differences between males and females. Contrary to the hypothesis that could be formed at first sight, the variability in weight increases considerably, in almost all cases, when the degree of homozygosity increases. Here again quite considerable differences are found in the evolution of the variability with the degree of homozygosity, from one muscle to the other and also between the two sexes. Comparison of the mean weight of the left and right elements of the bilateral muscles shows no significant preponderance. It was found, however, that slight asymmetries observed in the different groups of different consanguinity tend to be in the same direction for a given muscle. The variability of the weights of the left and right elements does not seem to be influenced by the degree of homozygosity in the females; in the males, however, an increase in homozygosity increases the variability of the weights of the left and right elements in certain cases. The mean degree of humidity and the variability of the ratio wet weight/dry weight are not changed significantly by the degree of consanguinity in females. In the males, the variability in the degree of humidity is less in heterozygotes, an indication of their better capacity for homeostatic regulation. The reduction in the mean weights and the increase in variability as the degree of homozygosity increases shows the importance of the advantage of heterozygotes, which has a bearing on theories of the genetics of populations and their application in rearing, and particularly to selection techniques.     

Structure and Stability of Human Telomeric G-Quadruplex with Preclinical 9-Amino Acridines

G-quadruplexes are higher-order DNA structures formed from guanine-rich sequences, and have been identified as attractive anticancer drug targets. Elucidating the three-dimensional structure of G-quadruplex with 9-amino acridines and the specific interactions involved in binding selectivity are the key to understanding their mechanism of action. Fluorescence titration assays, competitive dialysis and NMR studies have been used to study the binding specificity of 9-amino acridines to DNA. Structural models of the complexes with the telomeric DNA G-quadruplex based on NMR measurements were developed and further examined by molecular dynamics simulations and free energy calculations. Selective binding of 9-amino acridines for G-quadruplex sequences were observed. These compounds bind between A and G-tetrads, involving significant π-π interactions and several strong hydrogen bonds. The specific interactions between different moieties of the 9-amino acridines to the DNA were examined and shown to play a significant role in governing the overall stabilities of DNA G-quadruplex complexes. Both 9-amino acridines, with similar binding affinities to the G-quadruplex, were shown to induce different level of structural stabilization through intercalation. This unique property of altering structural stability is likely a contributing factor for affecting telomerase function and, subsequently, the observed differences in the anticancer activities between the two 9-amino acridines.