Self-organization in biological systems
Dislodged mussel on sandy sediment.
Self-organized systems create patterns resulting from interactions between components. Mónica López Pereira et al. (pp. 7975–7980) evaluated intraspecific interference-driven self-organization in sunflower stands. The authors cultivated sunflower plants in rows at the typical commercial density of 5.1 plants per m2 and higher densities of 10 and 14 plants per m2. At the higher densities, the authors observed neighboring plants in each row inclining in opposite directions toward favorable light environments. This pattern was triggered by pioneer plants that led to a wave of alternate inclinations that persisted until the stand reached maturity. Using shades of various transmission spectra and low red/far-red light beamed horizontally on the rows, the authors found that this pattern of self-organization might be attributed to a response by phytochromes to changes in the red/far-red ratio of light incident on the plants. Further, self-organized, high-density sunflower stands yielded 19–47% more oil per unit land area, compared with stands that were forced to remain in the upright position. Importantly, genetic variability for the intensity of this response was found among hybrids, paving a potential path toward the selection of this attribute by plant breeders. In a related article, Hélène de Paoli et al. (pp. 8035–8040) examined how self-organized patterning of mussel beds (Mytilus edulis) on sandy intertidal flats influences bed persistence. Mussel beds exhibit a characteristic organization on two spatial scales. On a decimeter scale, mussels form regularly spaced clusters by actively moving around, and on a meter scale, mussels form regularly spaced bands driven by competition for algae. The authors examined the effects of the two types of patterns on ecosystem robustness by conducting field manipulations and constructing small-scale, large-scale, and a combination of small-scale and large-scale patterns to observe the persistence of mussel beds under the natural influences of wave disturbances and predation. Both small-scale and large-scale self-organization enhanced the persistence of mussel beds. The authors suggest that small-scale cluster patterns might help explain resistance against disturbances, whereas large-scale patterns facilitate the reformation of small-scale patterns when mussels are dislodged by waves. According to the authors, restoring and protecting the spatial pattern of ecosystems could enhance ecosystem resilience. — R.W.
Vertebrate population declines and sixth mass extinction
Barn swallows are a decreasing vertebrate listed as a species of “least concern,” according to the IUCN. Image courtesy of Flickr/Matt MacGillivray.
Accounts of human-caused biodiversity loss often highlight species extinctions but neglect the extinction of populations within species. To examine the magnitude of vertebrate population reduction, Gerardo Ceballos et al. (pp. E6089–E6096) mapped the ranges of 27,600 birds, amphibians, mammals, and reptiles worldwide at a 10,000-km2 scale. The sample represented nearly half of known terrestrial vertebrate species, and included the 8,851 species that are decreasing in population size and range, according to the International Union for Conservation of Nature (IUCN) as of March 2016. The authors found that the tropics had the greatest number of decreasing species, while temperate regions had similar or higher proportions of decreasing species than tropical regions. Furthermore, the authors found that approximately 30% of all decreasing species are considered common species and of low concern by the IUCN. Geographic analyses of 177 mammal species found that between approximately 1900 and 2015, all species had lost at least 30% of their geographic ranges and that more than 40% of the species had experienced more than 80% range reduction. According to the authors, Earth is not only experiencing accelerated human-driven species extinctions but also population declines and extirpations. — L.C.
Stem cell-loaded oncolytic virus and brain melanomas
Melanomas metastasize to the brain in about half of all melanoma patients, and no effective therapies exist for such patients. Wanlu Du et al. (pp. E6157–E6165) engineered human mesenchymal stem cells (MSCs) with oncolytic herpes simplex virus (oHSV), and demonstrated that oHSV-armed MSC (MSC-oHSV) injected via the internal carotid artery tracked and killed melanoma tumor cells in the mouse brain and significantly increased the survival of mice with metastatic melanoma tumors. The authors conducted the experiments in clinically relevant mouse models of melanoma brain metastasis developed from BRAF mutant and wild-type brain-seeking melanoma lines. The authors also investigated the efficacy of MSC-oHSV in combination with anti–PD-L1 immunotherapy in an immunocompetent mouse model of melanoma brain metastasis, and found that the combined therapy greatly increased mouse survival compared with either therapy alone. The results indicate that MSC-oHSV could be used to target and kill melanomas in the brain. According to the authors, the mouse models could serve as useful preclinical platforms to unravel melanoma brain metastasis and test therapeutic approaches. — S.R.
Paleocene bird fossil and avian evolution
Fossil bones of T. abini.
Molecular evidence suggests a rapid diversification of birds following the Cretaceous–Paleogene (K–Pg) mass extinction 66 million years ago. However, fossil evidence from this period has been lacking. Daniel Ksepka et al. (pp. 8047–8052) report on fossil remains of a previously undocumented arboreal bird species, Tsidiiyazhi abini, which was recovered from a 62.5-million-year-old rock layer in the Nacimiento Formation of New Mexico, making it the oldest known arboreal crown bird. Based on morphological features of the vertebra, wing, and foot bones, the authors assigned the bird to the order Coliiformes, or mousebirds, a classification supported by phylogenetic analysis of 111 morphological features in 48 extant and fossil bird species. The age of the T. abini fossil and the reconstructed evolutionary relationships between major landbird lineages suggest that as many as nine major bird clades diverged within 4 million years following the K–Pg extinction. T. abini also exhibits evidence of semizygodactyly, a specialized foot morphology, suggesting that evolution of such morphological, and therefore ecological, specializations had already begun by this time. The phylogenetic reconstruction also suggests that semizygodactyly evolved independently in three different clades and was not a precursor to full zygodactyly, according to the authors. — B.D.
Rapid and accurate HLA typing
Rapid HLA-typing algorithm could aid precision medicine. Image courtesy of iStockphoto/ktsimage.
Among the most diverse of genes in the human population, the human leukocyte antigen (HLA) gene complex, located on chromosome 6, plays crucial roles in autoimmunity, transplant rejection, and cancer, among other conditions. Because of the high degree of sequence similarity between polymorphic HLA genes, HLA types are difficult to determine accurately and rapidly using genome sequence data from current short-read sequencing methods. Chao Xie et al. (pp. 8059–8064) developed a sequencing algorithm called xHLA, which can predict HLA types from short-read sequencing data more rapidly and accurately than existing algorithms. The authors tested xHLA on four public datasets that included whole-genome and exome sequences, and found that it outperformed existing algorithms. Compared with other algorithms, which took 15 minutes to 5 hours for HLA typing, xHLA’s runtime was around 3 minutes for each whole-genome sample at 30× coverage under comparable conditions. In contrast to existing algorithms, xHLA uses protein-level sequence alignment, among other factors, resulting in a tidy and comprehensive alignment matrix and relatively greater prediction accuracy. Given the remarkable diversity of HLA genes among people and their central role in the immune system, xHLA might aid precision medicine by facilitating the development of a rapid and accurate test for HLA types from personal genome data, according to the authors. — P.N.