Fungi play major roles in ecosystem processes, but the determinants of fungal diversity and biogeographic patterns remain poorly understood. Using DNA metabarcoding data from hundreds of globally distributed soil samples, we demonstrate that fungal richness is decoupled from plant diversity. The plant-to-fungus richness ratio declines exponentially toward the poles. Climatic factors, followed by edaphic and spatial variables, constitute the best predictors of fungal richness and community composition at the global scale. Fungi show similar latitudinal diversity gradients to other organisms, with several notable exceptions. These findings advance our understanding of global fungal diversity patterns and permit integration of fungi into a general macroecological framework.
Carbohydrate-active enzymes (CAZymes) are very important to the biotech industry, particularly the emerging biofuel industry because CAZymes are responsible for the synthesis, degradation and modification of all the carbohydrates on Earth. We have developed a web resource, dbCAN (http://csbl.bmb.uga.edu/dbCAN/annotate.php), to provide a capability for automated CAZyme signature domain-based annotation for any given protein data set (e.g. proteins from a newly sequenced genome) submitted to our server. To accomplish this, we have explicitly defined a signature domain for every CAZyme family, derived based on the CDD (conserved domain database) search and literature curation. We have also constructed a hidden Markov model to represent the signature domain of each CAZyme family. These CAZyme family-specific HMMs are our key contribution and the foundation for the automated CAZyme annotation.
Cancer stem cells (CSCs) or tumor progenitor cells are involved in tumor progression and metastasis1. MicroRNAs (miRNAs) regulate both normal stem cells and CSCs2–5 and miRNA dysregulation has been implicated in tumorigenesis6. CSCs in many tumors, including cancers of the breast7, pancreas8, head and neck9, colon10,11, small intestine12, liver13, stomach14, bladder15, and ovary16 have been identified using adhesion molecule CD44, either individually or in combination with other marker(s). Prostate cancer (PCa) stem/progenitor cells with enhanced clonogenic17 and tumor-initiating and metastatic18,19 capacities are also enriched in the CD44+ cell population, but whether miRNAs regulate the CD44+ PCa cells and PCa metastasis remains unclear. Here we show, through expression analysis, that miR-34a, a p53 target20–24, was under-expressed in CD44+ PCa cells purified from xenograft and primary tumors. Enforced expression of miR-34a in bulk PCa cells inhibited clonogenic expansion and tumor development. miR-34a re-expression in CD44+ PCa cells blocked whereas miR-34a antagomirs in CD44− PCa cells promoted tumor regeneration and metastasis. Systemically delivered miR-34a inhibited PCa metastasis and extended animal survival. Of significance, CD44 was identified and validated as a direct and functional target of miR-34a and CD44 knockdown phenocopied miR-34a over-expression in inhibiting PCa regeneration and metastasis. Our study reveals miR-34a as a critical negative regulator of CD44+ PCa cells and establishes a strong rationale for developing miR-34a as a novel therapeutic against prostate CSCs.
Cell-cell communication in bacteria is accomplished through the exchange of extracellular signalling molecules called autoinducers. This process, termed quorum sensing, allows bacterial populations to coordinate gene expression. Community cooperation probably enhances the effectiveness of processes such as bioluminescence, virulence factor expression, antibiotic production and biofilm development. Unlike other autoinducers, which are specific to a particular species of bacteria, a recently discovered autoinducer (AI-2) is produced by a large number of bacterial species. AI-2 has been proposed to serve as a 'universal' signal for inter-species communication. The chemical identity of AI-2 has, however, proved elusive. Here we present the crystal structure of an AI-2 sensor protein, LuxP, in a complex with autoinducer. The bound ligand is a furanosyl borate diester that bears no resemblance to previously characterized autoinducers. Our findings suggest that addition of naturally occurring borate to an AI-2 precursor generates active AI-2. Furthermore, they indicate a potential biological role for boron, an element required by a number of organisms but for unknown reasons.
This manuscript describes a unique class of locomotive robot: A soft robot, composed exclusively of soft materials (elastomeric polymers), which is inspired by animals (e.g., squid, starfish, worms) that do not have hard internal skeletons. Soft lithography was used to fabricate a pneumatically actuated robot capable of sophisticated locomotion (e.g., fluid movement of limbs and multiple gaits). This robot is quadrupedal; it uses no sensors, only five actuators, and a simple pneumatic valving system that operates at low pressures (<10 psi). A combination of crawling and undulation gaits allowed this robot to navigate a difficult obstacle. This demonstration illustrates an advantage of soft robotics: They are systems in which simple types of actuation produce complex motion.biomimetic | mobile R obotics developed to increase the range of motions and functions open to machines, and to build into them some of the characteristics [including autonomous motion (1-3), adaptability to the environment (4-7), and capability of decision making (8, 9)] of animals, particularly animals with skeletons. Most mobile robots are built with hard materials (hard robots), either by adding treads or wheels (10, 11) to conventional machines to increase their mobility, or by starting with conceptual models based on animals [e.g., Big Dog (12) and many others (13-15)], and replicating some of their features in hard structures. Although robotics has made enormous progress in the last 50 years, hard robots still have many limitations. Some of these limitations are mechanical, and include instability when moving in difficult terrain; some have to do with the ranges of motions afforded by actuators and structures (e.g., metal rods, mechanical joints, and electric motors); some stem from the complexity in control (especially when handling materials and structures that are soft, delicate, and complex in shape). Hard robots fabricated from metals are also often heavy and expensive, and thus are not suitable for some applications.New classes of robots may thus find uses in applications where conventional hard robots are unsuitable. We are interested in a unique class of robots: That is, soft robots fabricated in materials (predominantly elastomeric polymers) that do not use a rigid skeleton to provide mechanical strength. The objective of this work is to demonstrate a soft robot that requires only simple design and control to generate mobility. In this demonstration, we begin to address some of the issues that have limited the development of soft robots. Instead of basing this and other designs on highly evolved animals as models, we are using simpler organisms [e.g., worms (16) and starfish (17)] for inspiration. These organisms, ones without internal skeletons, suggest designs that are simpler to make and are less expensive than conventional hard robots, and that may, in some respects, be more capable of complex motions and functions. Simple, inexpensive systems will probably not replace more complex and expensive ones, but may have different...
This study presents a radiomics nomogram that incorporates the radiomics signature, CT-reported LN status, and clinical risk factors, which can be conveniently used to facilitate the preoperative individualized prediction of LN metastasis in patients with CRC.
The excitement and controversy surrounding the potential role of human embryonic stem (ES) cells in transplantation therapy have often overshadowed their potentially more important use as a basic research tool for understanding the development and function of human tissues. Human ES cells can proliferate without a known limit and can form advanced derivatives of all three embryonic germ layers. What is less widely appreciated is that human ES cells can also form the extra-embryonic tissues that differentiate from the embryo before gastrulation. The use of human ES cells to derive early human trophoblast is particularly valuable, because it is difficult to obtain from other sources and is significantly different from mouse trophoblast. Here we show that bone morphogenetic protein 4 (BMP4), a member of the transforming growth factor-beta (TGF-beta) superfamily, induces the differentiation of human ES cells to trophoblast. DNA microarray, RT-PCR, and immunoassay analyses demonstrate that the differentiated cells express a range of trophoblast markers and secrete placental hormones. When plated at low density, the BMP4-treated cells form syncytia that express chorionic gonadotrophin (CG). These results underscore fundamental differences between human and mouse ES cells, which differentiate poorly, if at all, to trophoblast. Human ES cells thus provide a tool for studying the differentiation and function of early human trophoblast and could provide a new understanding of some of the earliest differentiation events of human postimplantation development.
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