Clusters and Graphs

Knowledge of the development and hierarchical organization of tissues is key to understanding how they are perturbed in injury and disease, as well as how they may be therapeutically manipulated to restore homeostasis. The rapidly regenerating intestinal epithelium harbors diverse cell types and their lineage relationships have been studied using numerous approaches, from classical label-retaining and genetic lineage tracing methods to novel transcriptome-based annotations. Here, we describe the developmental trajectories that dictate differentiation and lineage specification in the intestinal epithelium. We focus on the most recent single-cell RNA-sequencing (scRNA-seq)-based strategies for understanding intestinal epithelial cell lineage relationships, underscoring how they have refined our view of the development of this tissue and highlighting their advantages and limitations. We emphasize how these technologies have been applied to understand the dynamics of intestinal epithelial cells in homeostatic and injury-induced regeneration models.

A major topic of interest in human prehistory is how the large-scale genetic structure of modern populations outside of Africa was established. Demographic models have been developed that capture the relationships among small numbers of populations or within particular geographical regions, but constructing a phylogenetic tree with gene flow events for a wide diversity of non-Africans remains a difficult problem. Here, we report a model that provides a good statistical fit to allele-frequency correlation patterns among East Asians, Australasians, Native Americans, and ancient western and northern Eurasians, together with archaic human groups. The model features a primary eastern/western bifurcation dating to at least 45,000 years ago, with Australasians nested inside the eastern clade, and a parsimonious set of admixture events. While our results still represent a simplified picture, they provide a useful summary of deep Eurasian population history that can serve as a null model for future studies and a baseline for further discoveries.

Recent morphological and molecular data have shown that one of the most common parasites of freshwater fish in the Palaearctic Region, the cestode Caryophyllaeus laticeps (Pallas, 1781) (Eucestoda: Caryophyllidea), is highly polymorphic. Five distinct morphotypes of C. laticeps, largely corresponding to different fish hosts and representing separate, yet closely related genetic lineages, have been recognised and they are characterised in the present paper. Morphotype 1 from breams, Abramis brama (L.) (type-host) and Ballerus spp., corresponds to the original Taenia laticeps Pallas, 1781 and its neotype (paragenophore ex A. brama in Russia) is designated. This morphotype is characterised by a slender body and flabellate scolex. Morphotype 2 was found in the Macedonian vimba Vimba melanops (Heckel) and the vimba bream V. vimba (L.); it is typified by a more robust body, with most anterior extent of the vitelline follicles near the scolex and the cirrus-sac situated more anteriorly than in other morphotypes. Morphotype 3 is represented by worms from the common carp Cyprinus carpio L. that possess a cuneicrispitate scolex (having the form of a wedge with shallow indentations on anterior margin). Morphotype 4 from the common nase Chondrostoma nasus (L.) has a large, robust body and a wide scolex with numerous superficial grooves (wrinkles) in its anterior part. Morphotype 5 is represented by worms from the white-eye bream Ballerus sapa (Pallas); its typical characteristics are a festoon-like anterior margin of the scolex, the absence of vitelline follicles posterior to the cirrus-sac and the absence of a well-developed internal seminal vesicle. Discriminant analysis of 15 morphometric variables readily separated Morphotypes 3, 4 and 5 and confirmed the key discriminating power of traits related to the reproductive system, especially the terminal reproductive organs. Morphological polymorphism and the genetic divergence of different morphotypes of C. laticeps correspond to its wide spectrum of fish definitive hosts and a large distribution area that includes Europe, most of Palaearctic Asia and northern Africa.

Dual mycorrhizal symbiosis, i.e., the association with both arbuscular and ectomycorrhizal fungal symbionts, is an ambiguous phenomenon concurrently considered as common among various genetic lineages of trees and a result of bias in data analyses. Recent studies have shown that the ability to form dual mycorrhizal associations is a distinguishing factor for the continental-scale invasion of alien tree species. However, the phylogenetic mechanisms that drive it remain unclear. In this study, all the evidence on root-associated symbionts of Juglandaceae from South and North America, Asia, and Europe was combined and re-analysed following current knowledge and modern molecular-based identification methods. The Juglandaceae family was revealed to represent a specific pattern of symbiotic interactions that are rare among deciduous trees and absent among conifers. Closely related phylogenetic lineages of trees usually share the same type of symbiosis, but Juglandaceae contains several possible ones concurrently. The hyperdiversity of root symbionts of Juglandaceae, unlike other tree families, was concurrently found in Central and North America, Asia, and Europe, indicating its phylogenetic determinants, which endured geographical isolation. However, for many Juglandaceae, including the invasive Juglans and Pterocarya species, this was never studied or was studied only with outdated methods. Further molecular research on root symbionts of Juglandaceae, providing long sequences and high taxonomic resolutions, is required to explain their ecological roles.

The Republic of Buryatia (RB) is located southeast of Lake Baikal and shares a long border with Mongolia. This region of Russia was rabies-free from 1982 to 2010. The first outbreak of fox rabies in RB was identified in 2011, about 30km from the Russian-Mongolian border. We assessed the possible pathways to further spread the 'steppe' phylogenetic lineage of the rabies virus near the northeastern limits of its known distribution. All rabies cases were located 30-210km north of the Russia-Mongolia border, with a distance of up to 320km from each other. Rabies has spread to the north across steppe landscapes and river valleys, with foxes being the main natural hosts of the infection. All RABV isolates from RB belong to the 'steppe' phylogenetic lineage, and three major phylogenic groups could be separated. Group 1 contains sequences from RB, Mongolia, China (Inner Mongolia), and bordering regions of Russia. Group 2 is formed by isolates from other regions of Eastern Siberia, which have no borders with RB and foreign countries. Group 3 contains samples from Western Siberia with endemic fox rabies since the 1950s. The most probable cause of fox rabies epizooty in the RB was multiple drift of the RABV across the Russian-Mongolian border. Our data show that after 2010, fox rabies affected new areas in Central Asia and extended to the north and northeast. Affected areas are similar to the Mongolian-type steppes in their zoogeographical aspect. Closely related genetic lineages of RABV are circulating in RB, Mongolia and the nearest areas of China. International cooperation is necessary to prevent the spread of rabies in the bordering territories of these countries.

Born in Hanoi, Vietnam in 1952 and raised in Saigon Trinh T. Minh-ha received her schooling in music composition in Saigon before immigrating to the United States in 1970 for her higher education. In addition to her filmmaking, she composes music; creates multimedia installations, publishes on literary and film theory, feminism, and postcolonialism; and teaches at the University of California, Berkeley’s Gender and Women’s Studies Department. Trinh’s essay, literary, and theoretical work has been written about extensively by academics, and analysis of her films and her filmmaking has been greatly influential in visual ethnography studies. Trinh’s films also have been favored by postcolonial, feminist, and essay-film theorists, with some resistance from theorists of African postcolonialism for her outsider perspective and some resistance from feminism theorists for her participation in the very models of narrative and representation that she works to challenge. In opposition to these criticisms, many theorists have written defenses of Trinh’s work and process. Trinh herself has also given interviews and written essays that acknowledge that her work necessarily incites these criticisms. Trinh’s films take the form of ethnographic documentary, political documentary, essay film, and allegorical feature film, and they travel between Africa, Asia, and North America. In her work, she revisits themes of postcolonialism and neocolonialism, translation, multiplicity of identity, feminism, filmmaking itself, and, in more recent years, the digital turn. Trinh’s films emphasize process and ambiguity over direct message, and so her films tend to be formally essayistic, analyzing or thinking through subjects and theories as they are presented. In this way, her films have often been described by critics as genre crossing and hybrid. Like other female filmmakers who aim to garner some control over their image and their professional reception, Trinh has republished her creative work (as still images, scripts, and installation programs) and select interviews in several collections. These books also provide select bibliographies of reviews, additional interviews, and articles on Trinh’s work.

I consider the life of Georgia O'Keeffe (1887-1986), American Modernist painter and writer, as a series of windows through which she looks at the world and, at different stages, force and nourish the conquest of her identity as American, woman and artist. From the places of her childhood to the opaque period of 'confine' in New York, as Stieglitz’s wife and woman-artist, O’Keeffe plans her evasion, looking for a space of her own where to find the center of her individuality. The opening to the world is embodied in the multiple perspectives that New Mexico offers, in its physical and mental spaces. At Ghost Ranch, and in Abiquiu, O'Keeffe finds the natural sources of a work that brings back originality and discipline. The present work, articulated within visual studies, literature and culture, considers O’Keeffe’s modernism from a new transcendentalist perspective. The analysis is based on a selection of letters between O'Keeffe and Stieglitz (1913-1946), O'Keeffe and Maria Chabot (1941-1949), on his autobiography (1976), and conversations recorded in C.S.Merril’s Weekends with O'Keeffe (1973-1979), supported by selected images. I assert that the windows in New Mexico, even if only virtually told in letters, 'mimetic' and 'simulacral’, as in Friedberg’s The Virtual Window, turn out as bold openings in communion with the surrounding nature, and allow the artist to create the necessary exchange to live a collective individuality. O'Keeffe learns that this opening is the vehicle to honor her mission, the filter to better understand herself, protected by the reassuring domesticity, and the positive role model that, in the variations and repetitions of the simplicity of the daily rituals, restores her original relationship with the universe.

Literature used to be a great source of material for language teaching when it was the heyday of the grammar-translation approach. However, its inherent linguistic complexity and the practicality of the emerging CLT approach to language teaching split language practitioners: while some turn their back on literature, others find it useful as an authentic source for language use and creativity. In the EFL context, the inclusion of English literature in language classes for language development purposes has resulted in teachers’ dilemma about the balance between teaching literature as a study and teaching it for language study purposes. This study examines how teachers of English literature at a university of foreign languages in Central Vietnam used literary works in their EFL-majoring classes and what benefits and challenges they encountered while teaching literature to EFL students in language classrooms. The study employs a qualitative research design, with relevant data being collected through structured interviews and teachers’ critical reflections. The findings showed that teachers’ approaches to literary works varied depending on literary text types and teachers’ preferences, but they tended to focus on students’ evaluation of literary beauty, their understanding of socio-cultural life, and their responses to the situation in the works. Activities to promote language proficiency were mainly oral discussion, integrated into analysis and discussion tasks. Considering the benefits of teaching English literature in an EFL setting, teachers found that they could raise students’ intercultural awareness, develop students’ critical thinking and literary competence through life-like situations in the literary works. However, the findings also gave rise to the challenges of focusing on the cultural model of teaching literature, thereby hindering the attainment of language knowledge and skills. The study implies the significance of assertive learning objectives and outcomes.

Mammalian heart development requires precise allocation of cardiac progenitors. The existence of a multipotent progenitor for all anatomic and cellular components of the heart has been predicted but its identity and contribution to the two cardiac progenitor ‘fields’ has remained undefined. Here we show, using clonal genetic fate mapping, that Mesp1+ cells in gastrulating mesoderm are rapidly specified into committed cardiac precursors fated for distinct anatomic regions of the heart. We identify Smarcd3 as a marker of early specified cardiac precursors and identify within these precursors a compartment boundary at the future junction of the left and right ventricles that arises prior to morphogenesis. Our studies define the timing and hierarchy of cardiac progenitor specification and demonstrate that the cellular and anatomical fate of mesoderm-derived cardiac cells is specified very early. These findings will be important to understand the basis of congenital heart defects and to derive cardiac regeneration strategies.DOI: http://dx.doi.org/10.7554/eLife.03848.001

Lineage Tracing Methods and the Kidney

A comparative analysis of the dynamics of Plasmodium relictum (GRW4) development in the blood during single and co-infections

Experimental evidence for hybridization of closely related lineages in Plasmodium relictum

The Real Filth in American Psycho