Trees on networks: resolving statistical patterns of phylogenetic similarities among interacting proteins

Background  

Phylogenies capture the evolutionary ancestry linking extant species. Correlations and similarities among a set of species are mediated by and need to be understood in terms of the phylogenic tree. In a similar way it has been argued that biological networks also induce correlations among sets of interacting genes or their protein products.     

Computational and Experimental Investigation of the Antimicrobial Peptide Cecropin XJ and its Ligands as the Impact Factors of Antibacterial Activity

Cecropin XJ, as a heat stable antimicrobial peptide (AMP), displayed broad bacteriostatic activities, effectively inhibited proliferation of cancer cells and induced cell apoptosis in vitro. However, it exhibited little hemolytic activity and very low cytotoxicity to erythrocytes and normal cells. Although exerts multiple remarkable bioactivities, the refined molecular conformation of native Cecropin XJ remains unsolved. The aim of the present study is to comprehensively investigate the physicochemical characteristics and structure-function relationship of this antimicrobial peptide by using a series of bioinformatics and experimental approaches. In this study, we revealed that the mature Cecropin XJ consists of 41 amino acids, containing two α-helical structures from Lys⁷ to Lys²⁵ and from Ala²⁹ to Ile³⁹. The phylogenetic tree indicated that Cecropin XJ belongs to the Class I AMPs of cecropin family. Hydrophobic analysis showed Cecropin XJ is a typical amphiphilic molecule. The surface of Cecropin XJ was found to have a much wide range of electrostatic potential from ?83.243 to +83.243. The amphipathicity and surface potential of Cecropin XJ partially supported the AMP pore-forming hypothesis. Scanning electron microscopy experimentally confirmed the damages of Cecropin XJ to microbial membrane. Four predicted docking sites respectively for magnesium ion (Mg²⁺), adenosine diphosphate (ADP), bacteriopheophytin (BPH), and guanosine triphosphate (GTP) were found on the surface of Cecropin XJ. Thereinto, Mg²⁺ was experimentally proved to suppress the antibacterial activity of Cecropin XJ; both GTP and ADP enhanced the bactericidal activities to varying degrees. The present study provides a foundation for further investigation of molecular evolution, structural modification, and functional mechanisms of Cecropin XJ.     

Distinguishing Drift and Selection Empirically: “The Great Snail Debate” of the 1950s

Biologists and philosophers have been extremely pessimistic about the possibility of demonstrating random drift in nature, particularly when it comes to distinguishing random drift from natural selection. However, examination of a historical case – Maxime Lamotte’s study of natural populations of the land snail, Cepaea nemoralis in the 1950s – shows that while some pessimism is warranted, it has been overstated. Indeed, by describing a unique signature for drift and showing that this signature obtained in the populations under study, Lamotte was able to make a good case for a significant role for␣drift. It may be difficult to disentangle the causes of drift and selection acting in a population, but it is not (always) impossible.     

Possible explanation of the disparity between the in vitro and in vivo measurements of Rubisco activity: a study in loblolly pine grown in elevated pCO2.

Rubisco activity can be measured using gas exchange (in vivo) or using in vitro methods. Commonly in vitro methods yield activities that are less than those obtained in vivo. Rubisco activity was measured both in vivo and in vitro using a spectrophotometric technique in mature Pinus taeda L. (loblolly pine) trees grown using free-air CO2 enrichment in elevated (56 Pa) and current (36 Pa) pCO2. In addition, for studies where both in vivo and in vitro values of Rubisco activity were reported net CO2 uptake rate (A) was modelled based on the in vivo and in vitro values of Rubisco activity reported in the literature. Both the modelling exercise and the experimental data showed that the in vitro values of Rubisco activity were insufficient to account for the observed values of A. A trichloroacetic acid (TCA) precipitation of the protein from samples taken in parallel with those used for activity analysis was co-electrophoresed with the extract used for determining in vitro Rubisco activity. There was significantly more Rubisco present in the TCA precipitated samples, suggesting that the underestimation of Rubisco activity in vitro was attributable to an insufficient extraction of Rubisco protein prior to activity analysis. Correction of in vitro values to account for the under-represented Rubisco yielded mechanistically valid values for Rubisco activity. However, despite the low absolute values for Rubisco activity determined in vitro, the trends reported with CO2 treatment concurred with, and were of equal magnitude to, those observed in Rubisco activity measured in vivo.     

THE ZOOSPORE OF CHLOROKYBUS ATMOPHYTICUS,A CHAROPHYTE WITH SARCINOID GROWTH HABIT

Chlorokybus atmophyticus has a sarcinoid growth habit and produces scale-covered zoospores. Flagella are laterally inserted and attached internally to a multilayered structure characteristic of the Charophyceae. There are two kinds of pyrenoid in each cell, a feature previously observed in only one scaly green flagellate. C. atmophyticus demonstrates that the sarcinoid growth habit arose independently at least twice in the green algae and cannot be used to define taxonomic groups unless combined with other criteria. It is further concluded that C. atmophyticus should be classified in a separate family Chlorokybaceae and a separate order Chloroky bales.     

Interactions Among Fuel Management,Species Composition,Bark Beetles,and Climate Change and the Potential Effects on Forests of the Lake Tahoe Basin

Climate-driven increases in wildfires, drought conditions, and insect outbreaks are critical threats to forest carbon stores. In particular, bark beetles are important disturbance agents although their long-term interactions with future climate change are poorly understood. Droughts and the associated moisture deficit contribute to the onset of bark beetle outbreaks although outbreak extent and severity is dependent upon the density of host trees, wildfire, and forest management. Our objective was to estimate the effects of climate change and bark beetle outbreaks on ecosystem carbon dynamics over the next century in a western US forest. Specifically, we hypothesized that (a) bark beetle outbreaks under climate change would reduce net ecosystem carbon balance (NECB) and increase uncertainty and (b) these effects could be ameliorated by fuels management. We also examined the specific tree species dynamics—competition and release—that determined NECB response to bark beetle outbreaks. Our study area was the Lake Tahoe Basin (LTB), CA and NV, USA, an area of diverse forest types encompassing steep elevation and climatic gradients and representative of mixed-conifer forests throughout the western United States. We simulated climate change, bark beetles, wildfire, and fuels management using a landscape-scale stochastic model of disturbance and succession. We simulated the period 2010–2100 using downscaled climate projections. Recurring droughts generated conditions conducive to large-scale outbreaks; the resulting large and sustained outbreaks significantly increased the probability of LTB forests becoming C sources over decadal time scales, with slower-than-anticipated landscape-scale recovery. Tree species composition was substantially altered with a reduction in functional redundancy and productivity. Results indicate heightened uncertainty due to the synergistic influences of climate change and interacting disturbances. Our results further indicate that current fuel management practices will not be effective at reducing landscape-scale outbreak mortality. Our results provide critical insights into the interaction of drivers (bark beetles, wildfire, fuel management) that increase the risk of C loss and shifting community composition if bark beetle outbreaks become more frequent.