Ecological niche models in phylogeographic studies: applications,advances and precautions

The increased availability of spatial data and methodological developments in species distribution modelling has lead to concurrent advances in phylogeography, broadening the scope of questions studied, as well as providing unprecedented insights. Given the species‐specific nature of the information provided by ecological niche models (ENMs), whether it is on the environmental tolerances of species or their estimated distribution, today or in the past, it is perhaps not surprising that ENMs have rapidly become a common tool in phylogeographic analysis. Such information is essential to phylogeographic tests that provide important biological insights. Here, we provide an overview of the different applications of ENMs in phylogeographic studies, detailing specific studies and highlighting general limitations and challenges with each application. Given that the full potential of integrating ENMs into phylogeographic cannot be realized unless the ENMs themselves are carefully applied, we provide a summary of best practices with using ENMs. Lastly, we describe some recent advances in how quantitative information from ENMs can be integrated into genetic analyses, illustrating their potential use (and key concerns with such implementations), as well as promising areas for future development.     

Live-cell microscopy reveals small molecule inhibitor effects on MAPK pathway dynamics

Oncogenic mutations in the mitogen activated protein kinase (MAPK) pathway are prevalent in human tumors, making this pathway a target of drug development efforts. Recently, ATP-competitive Raf inhibitors were shown to cause MAPK pathway activation via Raf kinase priming in wild-type BRaf cells and tumors, highlighting the need for a thorough understanding of signaling in the context of small molecule kinase inhibitors. Here, we present critical improvements in cell-line engineering and image analysis coupled with automated image acquisition that allow for the simultaneous identification of cellular localization of multiple MAPK pathway components (KRas, CRaf, Mek1 and Erk2). We use these assays in a systematic study of the effect of small molecule inhibitors across the MAPK cascade either as single agents or in combination. Both Raf inhibitor priming as well as the release from negative feedback induced by Mek and Erk inhibitors cause translocation of CRaf to the plasma membrane via mechanisms that are additive in pathway activation. Analysis of Erk activation and sub-cellular localization upon inhibitor treatments reveals differential inhibition and activation with the Raf inhibitors AZD628 and GDC0879 respectively. Since both single agent and combination studies of Raf and Mek inhibitors are currently in the clinic, our assays provide valuable insight into their effects on MAPK signaling in live cells.     

Amputation induces stem cell mobilization to sites of injury during planarian regeneration

How adult stem cell populations are recruited for tissue renewal and repair is a fundamental question of biology. Mobilization of stem cells out of their niches followed by correct migration and differentiation at a site of tissue turnover or injury are important requirements for proper tissue maintenance and regeneration. However, we understand little about the mechanisms that control this process, possibly because the best studied vertebrate adult stem cell systems are not readily amenable to in vivo observation. Furthermore, few clear examples of the recruitment of fully potent stem cells, compared with limited progenitors, are known. Here, we show that planarian stem cells directionally migrate to amputation sites during regeneration. We also show that during tissue homeostasis they are stationary. Our study not only uncovers the existence of specific recruitment mechanisms elicited by amputation, but also sets the stage for the systematic characterization of evolutionarily conserved stem cell regulatory processes likely to inform stem cell function and dysfunction in higher organisms, including humans.     

Molecular and physiological properties associated with zebra complex disease in potatoes and its relation with Candidatus Liberibacter contents in psyllid vectors

Zebra complex (ZC) disease on potatoes is associated with Candidatus Liberibacter solanacearum (CLs), an α-proteobacterium that resides in the plant phloem and is transmitted by the potato psyllid Bactericera cockerelli (?ulc). The name ZC originates from the brown striping in fried chips of infected tubers, but the whole plants also exhibit a variety of morphological features and symptoms for which the physiological or molecular basis are not understood. We determined that compared to healthy plants, stems of ZC-plants accumulate starch and more than three-fold total protein, including gene expression regulatory factors (e.g. cyclophilin) and tuber storage proteins (e.g., patatins), indicating that ZC-affected stems are reprogrammed to exhibit tuber-like physiological properties. Furthermore, the total phenolic content in ZC potato stems was elevated two-fold, and amounts of polyphenol oxidase enzyme were also high, both serving to explain the ZC-hallmark rapid brown discoloration of air-exposed damaged tissue. Newly developed quantitative and/or conventional PCR demonstrated that the percentage of psyllids in laboratory colonies containing detectable levels of CLs and its titer could fluctuate over time with effects on colony prolificacy, but presumed reproduction-associated primary endosymbiont levels remained stable. Potato plants exposed in the laboratory to psyllid populations with relatively low-CLs content survived while exposure of plants to high-CLs psyllids rapidly culminated in a lethal collapse. In conclusion, we identified plant physiological biomarkers associated with the presence of ZC and/or CLs in the vegetative potato plant tissue and determined that the titer of CLs in the psyllid population directly affects the rate of disease development in plants.     

Amplistroma longicollis, a new species and its anamorph state described and sequenced from Europe

The new species Amplistroma longicollis is described. It is characterized by pale to dark brown stromata covered with white mucilaginous exudates and rostrate long-necked perithecia, which also present mucilaginous exudates at the base. Its relationship with other species of the genera Amplistroma in the Amplistromataceae is studied with morphological, cultural and molecular sequence data of large subunit ribosomal DNA (28S rDNA) and elongation factor 1-alpha gene (ef1-alpha).     

Pigment dispersing hormone modulates spontaneous electrical activity of the cerebroid ganglion and synchronizes electroretinogram circadian rhythm in crayfish Procambarus clarkii

In crayfish, one very well-studied circadian rhythm is that of electroretinogram (ERG) amplitude. The cerebroid ganglion has been considered a plausible site for the circadian pacemaker of this rhythm and for the retinular photoreceptors, as the corresponding effectors. The pigment dispersing hormone (PDH) appears to synchronize ERG rhythm, but its characterization as a synchronizer cue remains incomplete. The main purposes of this work were a) to determine whether PDH acts on the cerebroid ganglion, and b) to complete its characterization as a non-photic synchronizer. Here we show that PDH increases the number of the spontaneous potentials of the cerebroid ganglion, reaching 149.92 ± 6.42% of the activity recorded in the controls, and that daily application of PDH for 15 consecutive days adjusts the ERG circadian rhythm period to 24.0 ± 0.2 h and the end of the activity period of the rhythm coincides with the injection of the hormone. In this work, we hypothesized that in crayfish, PDH transmits the “day” signal to the ERG circadian system and acts upon both the presumptive circadian pacemaker and the corresponding effectors to reinforce the synchronization of the system.     

Temporal competition between differentiation programs determines cell fate choice

Multipotent differentiation, where cells adopt one of several possible fates, occurs in diverse systems ranging from bacteria to mammals. This decision‐making process is driven by multiple differentiation programs that operate simultaneously in the cell. How these programs interact to govern cell fate choice is poorly understood. To investigate this issue, we simultaneously measured activities of the competing sporulation and competence programs in single Bacillus subtilis cells. This approach revealed that these competing differentiation programs progress independently without cross‐regulation before the decision point. Cells seem to arrive at a fate choice through differences in the relative timing between the two programs. To test this proposed dynamic mechanism, we altered the relative timing by engineering artificial cross‐regulation between the sporulation and competence circuits. Results suggest a simple model that does not require a checkpoint or intricate cross‐regulation before cellular decision‐making. Rather, cell fate choice appears to be the outcome of a ‘molecular race’ between differentiation programs that compete in time, providing a simple dynamic mechanism for decision‐making.     

Succession of a Southern Appalachian Mountain Wetland Six Years following Hydrologic and Microtopographic Restoration

Microtopography, which is known to play a key role in the structure and function of wetland communities, is receiving increasing attention in wetland restoration projects. One goal of the Tulula Wetlands Mitigation Bank, which was the first large-scale wetland restoration project in the Blue Ridge Province, was to restore the microtopography in a degraded swamp forest–bog complex. This wetland type has become increasingly rare in the southern Appalachians and is characterized by a distinct microtopography of depressions and low ridges. We examined vegetation and soils in depression and ridge plots over a 6-year period, during which the hydrology and microtopography of the floodplain were restored. Our results showed that the flora of the depression and ridge plots differed, with greater coverage by obligate wetland species in the depression plots but greater overall taxonomic richness in the ridge plots. The edaphic characteristics that we measured varied very little during the study period. Creating microtopographic relief during the restoration of this wetland seems to have provided a variety of niches and may have increased the likelihood that the site will succeed back to a swamp forest–bog complex, rather than as a forested terrace of Tulula Creek.