Breeding latitude leads to different temporal but not spatial organization of the annual cycle in a long‐distance migrant

The temporal and spatial organization of the annual cycle according to local conditions is of crucial importance for individuals’ fitness. Moreover, which sites and when particular sites are used can have profound consequences especially for migratory animals, because the two factors shape interactions within and between populations, as well as between animal and the environment. Here, we compare spatial and temporal patterns of two latitudinally separated breeding populations of a trans‐Equatorial passerine migrant, the collared flycatcher Ficedula albicollis, throughout the annual cycle. We found that migration routes and non‐breeding residency areas of the two populations largely overlapped. Due to climatic constraints, however, the onset of breeding in the northern population was approximately two weeks later than that of the southern population. We demonstrate that this temporal offset between the populations carries‐over from breeding to the entire annual cycle. The northern population was consistently later in timing of all subsequent annual events – autumn migration, non‐breeding residence period, spring migration and the following breeding. Such year‐round spatiotemporal patterns suggest that annual schedules are endogenously controlled with breeding latitude as the decisive element pre‐determining the timing of annual events in our study populations.     

Can pollination syndromes indicate ecological restoration success in tropical forests?

We evaluated the pollination syndromes of plant species occurring in revegetated patches of riparian Atlantic Forest in order to evaluate the success of restoration process. Between March 2013 and January 2014, the floral traits of all of the flowering plants found in, among four restoration sites of different ages and one reference site, were recorded and used to characterize pollination syndromes. Richness, abundance, and composition of pollination syndromes were related to season, age and width of the forest fragment, species richness and abundance of sampled plants, and also to the quality of the surrounding matrix. There were differences in the composition of syndromes among sampling units and among seasons. Richness and abundance of pollination syndromes varied among climatic periods, the highest values occurred at the end of the dry season and the start of the rainy season. Older, wider, and areas with more plants had higher values of richness and abundance of syndromes. The quality of the surrounding matrix influences only the richness of syndromes. It was concluded that floral traits are good indicators of ecological restoration of riparian forests and that the surrounding matrix contributes to the greater richness of syndromes. However, when planning for active restoration, attention should be given to the proper choice of plant species on the basis of pollination syndromes that should attract pollinators.     

Enhancement of the Amazonian Açaí Waste Fibers through Variations of Alkali Pretreatment Parameters

The açaí fruit depulping produces large amounts of long lignocellulosic fiber bundles that are disposed in the environment. Chemical pretreatments may improve açaí fibers favoring their usage in advanced materials. This work aimed to define optimal alkali reaction parameters to improve the properties of açaí fibers. Two NaOH concentrations (5 % and 10 %) and two reaction temperatures (80 °C and 100 °C) were tested. The raw and treated fibers were analyzed by scanning electron microscopy, Fourier transformed infrared spectroscopy, X‐ray diffraction, and thermal analyses. All the alkali pretreatments separated fibers from the bundles, unblocked pit channels by removing silicon structures, exposed the inner lignin, partially removed non‐cellulosic compounds, and raised the cellulose crystalline index. The highest temperature and NaOH content resulted in better cleaning and isolation of the fibers, while milder conditions better preserved the cellulose crystalline structure and thermal stability.     

HPV18 Utilizes Two Alternative Branch Sites for E6~*I Splicing to Produce E7 Protein

Human papillomavirus 18(HPV18) E6 and E7 oncogenes are transcribed as a single bicistronic E6 E7 pre-mRNA. The E6 ORF region in the bicistronic E6 E7 pre-mRNA contains an intron. Splicing of this intron disrupts the E6 ORF integrity and produces a spliced E6~*I RNA for efficient E7 translation. Here we report that the E6 intron has two overlapped branch point sequences(BPS) upstream of its 30 splice site, with an identical heptamer AACUA■C, for E6~*I splicing. One heptamer has a branch site adenosine(underlined) at nt 384 and the other at nt 388. E6~*I splicing efficiency correlates to the expression level of E6 and E7 proteins and depends on the selection of which branch site. In general, E6~*I splicing prefers the 30 ss-proximal branch site at nt 388 over the distal branch site at nt 384. Inactivation of the nt 388 branch site was found to activate a cryptic acceptor site at nt 636 for aberrant RNA splicing. Together, these data suggest that HPV18 modulates its production ratio of E6 and E7 proteins by alternative selection of the two mapped branch sites for the E6~*I splicing, which could be beneficial in its productive or oncogenic infection according to the host cell environment.     

Have the cake and eat it: Optimizing nondestructive DNA metabarcoding of macroinvertebrate samples for freshwater biomonitoring

DNA metabarcoding can contribute to improving cost‐effectiveness and accuracy of biological assessments of aquatic ecosystems, but significant optimization and standardization efforts are still required to mainstream its application into biomonitoring programmes. In assessments based on freshwater macroinvertebrates, a key challenge is that DNA is often extracted from cleaned, sorted and homogenized bulk samples, which is time‐consuming and may be incompatible with sample preservation requirements of regulatory agencies. Here, we optimize and evaluate metabarcoding procedures based on DNA recovered from 96% ethanol used to preserve field samples and thus including potential PCR inhibitors and nontarget organisms. We sampled macroinvertebrates at five sites and subsampled the preservative ethanol at 1 to 14 days thereafter. DNA was extracted using column‐based enzymatic (TISSUE) or mechanic (SOIL) protocols, or with a new magnetic‐based enzymatic protocol (BEAD), and a 313‐bp COI fragment was amplified. Metabarcoding detected at least 200 macroinvertebrate taxa, including most taxa detected through morphology and for which there was a reference barcode. Better results were obtained with BEAD than SOIL or TISSUE, and with subsamples taken 7–14 than 1–7 days after sampling, in terms of DNA concentration and integrity, taxa diversity and matching between metabarcoding and morphology. Most variation in community composition was explained by differences among sites, with small but significant contributions of subsampling day and extraction method, and negligible contributions of extraction and PCR replication. Our methods enhance reliability of preservative ethanol as a potential source of DNA for macroinvertebrate metabarcoding, with a strong potential application in freshwater biomonitoring.     

Cryptic phenology in plants: Case studies,implications, and recommendations

Plant phenology—the timing of cyclic or recurrent biological events in plants—offers insight into the ecology, evolution, and seasonality of plant‐mediated ecosystem processes. Traditionally studied phenologies are readily apparent, such as flowering events, germination timing, and season‐initiating budbreak. However, a broad range of phenologies that are fundamental to the ecology and evolution of plants, and to global biogeochemical cycles and climate change predictions, have been neglected because they are “cryptic”—that is, hidden from view (e.g., root production) or difficult to distinguish and interpret based on common measurements at typical scales of examination (e.g., leaf turnover in evergreen forests). We illustrate how capturing cryptic phenology can advance scientific understanding with two case studies: wood phenology in a deciduous forest of the northeastern USA and leaf phenology in tropical evergreen forests of Amazonia. Drawing on these case studies and other literature, we argue that conceptualizing and characterizing cryptic plant phenology is needed for understanding and accurate prediction at many scales from organisms to ecosystems. We recommend avenues of empirical and modeling research to accelerate discovery of cryptic phenological patterns, to understand their causes and consequences, and to represent these processes in terrestrial biosphere models.     

Substrate‐dependent cluster density dynamics of Corynebacterium glutamicum phosphotransferase system permeases

Many bacteria take up carbohydrates by membrane‐integral sugar specific phosphoenolpyruvate‐dependent carbohydrate:phosphotransferase systems (PTS). Although the PTS is centrally involved in regulation of carbon metabolism in different bacteria, little is known about localization and putative oligomerization of the permease subunits (EII). Here, we analyzed localization of the fructose specific PtsF and the glucose specific PtsG transporters, as well as the general components EI and HPr from Corynebacterium glutamicum using widefield and single molecule localization microscopy. PtsF and PtsG form membrane embedded clusters that localize in a punctate pattern. Size, number and fluorescence of the membrane clusters change upon presence or absence of the transported substrate, and a direct influence of EI and HPr was not observed. In presence of the transport substrate, EII clusters significantly increased in size. Photo‐activated localization microscopy data revealed that, in presence of different carbon sources, the number of EII proteins per cluster remains the same, however, the density of these clusters reduces. Our work reveals a simple mechanism for efficient membrane occupancy regulation. Clusters of PTS EII transporters are densely packed in absence of a suitable substrate. In presence of a transported substrate, the EII proteins in individual clusters occupy larger membrane areas.