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The article discusses about Genetic modifications of organisms can create artificial, synthetic genomes. Such changes are forecast to be useful for understanding the principles of how genomic context affects cellular function. However, the effects of most drastic genomic movements are unknown, never having been observed in nature. Brooks et al. examined a line of yeast that are easily induced to move genes within the genome.

The article focuses on the impact of policy actions on biodiversity outcomes and how this supports policy goals. It mentions about the need for scientific advances to investigate what levels of biodiversity loss are damaging for ecosystem functioning, and to fill knowledge gaps about the complex interactions between species extinctions, biodiversity, ecosystem functioning, and ecosystem services.

The article discusses United Nations (UN) policy processes are embracing access and benefit sharing (ABS) policy approach to biological conservation and equity in science. It mentions that several countries are negotiating a treaty under the United Nations Convention on the Law of the Sea (UNCLOS) to address governance gaps in the conservation and sustainable use of marine biological diversity in areas beyond national jurisdiction (ABNJ).

The article discusses that a survivor of the quaternary glacial period, the Sichuan taimen is a valuable genetic resource with scientific value for studying animal geography, paleoecology, and climate change. To protect the Sichuan taimen, the Chinese government should understand the risks of its extinction and should designate the spawning sites as natural reserves.

Despite decades of work by structural biologists, there are still ~5200 protein families with unknown structure outside the range of comparative modeling. We show that Rosetta structure prediction guided by residue-residue contacts inferred from evolutionary information can accurately model proteins that belong to large families and that metagenome sequence data more than triple the number of protein families with sufficient sequences for accurate modeling.We then integrate metagenome data, contact-based structure matching, and Rosetta structure calculations to generate models for 614 protein families with currently unknown structures; 206 are membrane proteins and 137 have folds not represented in the Protein Data Bank. This approach provides the representative models for large protein families originally envisioned as the goal of the Protein Structure Initiative at a fraction of the cost. [ABSTRACT FROM AUTHOR]

Telomerase helps maintain telomeres by processive synthesis of telomere repeat DNA at their 3'-ends, using an integral telomerase RNA (TER) and telomerase reverse transcriptase (TERT). We report the cryo-electron microscopy structure of Tetrahymena telomerase at ~9 angstrom resolution. In addition to seven known holoenzyme proteins, we identify two additional proteins that form a complex (TEB) with single-stranded telomere DNA-binding protein Teb1, paralogous to heterotrimeric replication protein A (RPA). The p75-p45-p19 subcomplex is identified as another RPA-related complex, CST (CTC1-STN1-TEN1). This study reveals the paths of TER in the TERT-TER-p65 catalytic core and single-stranded DNA exit; extensive subunit interactions of the TERT essential N-terminal domain, p50, and TEB; and other subunit identities and structures, including p19 and p45C crystal structures. Our findings provide structural and mechanistic insights into telomerase holoenzyme function. [ABSTRACT FROM AUTHOR]

The article discusses that Plants continuously adjust their body plans to adapt to the local environment by forming new organs in different developmental contexts. Underground, lateral roots initiate from designated cells in the pericycle of the main root. Aboveground, plants generate shoot-borne roots, bypassing the embryonic root-shoot lineage separation.

The article discusses Drosophila melanogaster has had a fruitful history in biological research because it has contributed tomany key discoveries in genetics, development, and neurobiology. The fruit fly genome contains ~14,000 proteincoding genes, ~63% of which have human orthologs. Single-cellRNA-sequencing has recently been applied to multiple Drosophila tissues and developmental stages.

The article discusses The Sichuan taimen (Hucho bleekeri), a glacial relict and freshwater salmonid fish endemic to the Yangtze River, has been categorized as Critically Endangered on the Red List of the International Union for Conservation of Nature and is listed as an endangered species on China's Species Red List. There are currently between 2000 and 2500 Sichuan taimen individuals, and the population is likely to decrease by more than 20% over the next two generations.

The article discusses that the cerebrovasculature delivers nourishment and regulates blood-brain molecular exchanges that are necessary for neurologic function. Coordinated communications between multiple cell types—including endothelium, pericytes, smooth muscle cells, and perivascular fibroblasts—provides the basis for the functional specialization of arteries, capillaries, and veins. Cellular dysfunction results in cerebrovascular diseases, a leading cause of death and disability.

The article discusses the Greek government banned road construction in six Natura 2000 roadless mountainous areas, triggering a broader national roadless policy. Road sprawl is a key catalyst of land use change, which is the greatest threat to biodiversity worldwide. For years, scientists have called for halting infrastructure expansion, including roads, to protect biodiversity, with little success. Greece's policy should serve as a model for the EU.

The article discusses that given that genome reading technologies have advanced to the point that human genomes can now be sequenced inexpensively within hours, it is not unreasonable to assume that genome writing technologies will follow suit. Even more challenging and timeconsuming than DNA writing is the debugging that synthetic genomes will likely require. Efficient genome writing will need to be tightly coupled to quality control.

Retroviral integrase (IN) functions within the intasome nucleoprotein complex to catalyze insertion of viral DNA into cellular chromatin. Using cryo–electron microscopy, we now visualize the functional maedi-visna lentivirus intasome at 4.9 angstrom resolution. The intasome comprises a homo-hexadecamer of IN with a tetramer-of-tetramers architecture featuring eight structurally distinct types of IN protomers supporting two catalytically competent subunits. The conserved intasomal core, previously observed in simpler retroviral systems, is formed between two IN tetramers, with a pair of C-terminal domains from flanking tetramers completing the synaptic interface. Our results explain how HIV-1 IN, which self-associates into higher-order multimers, can form a functional intasome, reconcile the bulk of early HIV-1 IN biochemical and structural data, and provide a lentiviral platform for design of HIV-1 IN inhibitors. [ABSTRACT FROM AUTHOR]

Genome-wide characterization of the in vivo cellular response to perturbation is fundamental to understanding how cells survive stress. Identifying the proteins and pathways perturbed by small molecules affects biology and medicine by revealing the mechanisms of drug action. We used a yeast chemogenomics platform that quantifies the requirement for each gene for resistance to a compound in vivo to profile 3250 small molecules in a systematic and unbiased manner. We identified 317 compounds that specifically perturb the function of 121 genes and characterized the mechanism of specific compounds. Global analysis revealed that the cellular response to small molecules is limited and described by a network of 45 major chemogenomic signatures. Our results provide a resource for the discovery of functional interactions among genes, chemicals, and biological processes. [ABSTRACT FROM AUTHOR]

The article reports that the Artificial intelligence (AI) solved one of biology grand challenges predicting how proteins fold from a chain of amino acids into 3D shapes that carry out life tasks. Topics include examines that body uses tens of thousands of different proteins, each a string of dozens to hundreds of amino acids; and considered that shapes helps researchers devise drugs that can lodge in proteins' crevices.

The article presents a study which reveals how human cancer cells thrive in the specialized anatomical location by hijacking a high-affinity iron transport system. It mentions that studying tumor cell properties in the context of the challenges posed by the microenvironment can reveal unknown biology and possible approaches to therapy; and disseminated cancer cells can reach the brain microvasculature, cross the blood-cerebrospinal fluid (CSF) barrier, and attach to the meninges.

DNA is thought to behave as a stiff elastic rod with respect to the ubiquitous mechanical deformations inherent to its biology. To test this model at short DNA lengths, we measured the mean and variance of end-to-end length for a series of DNA double helices in solution, using small-angle x-ray scattering interference between gold nanocrystal labels. In the absence of applied tension, DNA is at least one order of magnitude softer than measured by single-molecule stretching experiments. Further, the data rule out the conventional elastic rod model. The variance in end-to-end length follows a quadratic dependence on the number of base pairs rather than the expected linear dependence, indicating that DNA stretching is cooperative over more than two turns of the DNA double helix. Our observations support the idea of long-range allosteric communication through DNA structure. [ABSTRACT FROM AUTHOR]

We now have a wealth of information about the molecular signals that act on cells in embryos, but how do the control systems based on these signals generate pattern and govern the timing of developmental events? Here, I discuss four examples to show how mathematical modeling and quantitative experimentation can give some useful answers. The examples concern the Bicoid gradient in the early Drosophila embryo, the dorsoventral patterning of a frog embryo by bone morphogenetic protein signals, the auxin-mediated patterning of plant meristems, and the Notch-dependent somite segmentation clock. [ABSTRACT FROM AUTHOR]

Changes in gene regulation are thought to have contributed to the evolution of human development. However, in vivo evidence for uniquely human developmental regulatory function has remained elusive. In transgenic mice, a conserved noncoding sequence (HACNS1) that evolved extremely rapidly in humans acted as an enhancer of gene expression that has gained a strong limb expression domain relative to the orthologous elements from chimpanzee and rhesus macaque. This gain of function was consistent across two developmental stages in the mouse and included the presumptive anterior wrist and proximal thumb. In vivo analyses with synthetic enhancers, in which human-specific substitutions were introduced into the chimpanzee enhancer sequence or reverted in the human enhancer to the ancestral state, indicated that 13 substitutions clustered in an 81-base pair module otherwise highly constrained among terrestrial vertebrates were sufficient to confer the human-specific limb expression domain. [ABSTRACT FROM AUTHOR]

The biogeographic variation of life has predominantly been studied using taxonomy, but this focus is changing. There is a resurging interest in understanding patterns in the distribution not only of taxa but also of the traits those taxa possess. Patterns of trait variation shed light on fundamental questions in biology, including why organisms live where they do and how they will respond to environmental change. Technological advances such as environmental gehomics place microbial ecology in a unique position to move trait-based biogeography forward. We anticipate that as trait-based biogeography continues to evolve, micro- and macroorganisms will be studied in concert, establishing a science that is informed by and relevant to all domains of life. [ABSTRACT FROM AUTHOR]

Little is known about the way developmental cues affect how cells interpret their environment. We characterized the transcriptional response to high salinity of different cell Layers and developmental stages of the Arabidopsis root and found that transcriptional responses are highly constrained by developmental parameters. These transcriptional changes lead to the differential regulation of specific biological functions in subsets of cell layers, several of which correspond to observable physiological changes. We showed that known stress pathways primarily control semiubiquitous responses and used mutants that disrupt epidermal patterning to reveal cell-layer-specific and inter-cell-layer effects. By performing a similar analysis using iron deprivation, we identified common cell-type-specific stress responses and revealed the crucial role the environment plays in defining the transcriptional outcome of cell-fate decisions. [ABSTRACT FROM AUTHOR]

Initiation of actin polymerization in cells requires nucleation factors. Here we describe an actin-binding protein, leiomodin, that acted as a strong filament nucleator in muscle cells. Leiomodin shared two actin-binding sites with the filament pointed end-capping protein tropomodulin: a flexible N-terminal region and a leucine-rich repeat domain. Leiomodin also contained a C-terminal extension of 150 residues. The smallest fragment with strong nucleation activity included the leucine-rich repeat and C-terminal extension. The N-terminal region enhanced the nucleation activity threefold and recruited tropomyosin, which weakly stimulated nucleation and mediated localization of leiomodin to the middle of muscle sarcomeres. Knocking down leiomodin severely compromised sarcomere assembly in cultured muscle cells, which suggests a role for leiomodin in the nucleation of tropomyosin-decorated filaments in muscles. [ABSTRACT FROM AUTHOR]

PksA, which initiates biosynthesis of the environmental carcinogen aflatoxin B1, is one of the multidomain iterative polyketide synthases (IPKSs), a large, poorly understood family of biosynthetic enzymes. We found that dissection of PksA and its reconstitution from selected sets of domains allows the accumulation and characterization of advanced octaketide intermediates bound to the enzyme, permitting the reactions controlled by individual catalytic domains to be identified. A product template (PT) domain unites with the ketosynthase and thioesterase in this IPKS system to assemble precisely seven malonyl-derived building blocks to a hexanoyl starter unit and mediate a specific cyclization cascade. Because the PT domain is common among nonreducing IPKSs, these mechanistic features should prove to be general for IPKS-catalyzed production of aromatic polyketides. [ABSTRACT FROM AUTHOR]

Globally, priority areas for biodiversity are relatively well known, yet few detailed plans exist to direct conservation action within them, despite urgent need. Madagascar, like other globally recognized biodiversity hot spots, has complex spatial patterns of endemism that differ among taxonomic groups, creating challenges for the selection of within-country priorities. We show, in an analysis of wide taxonomic and geographic breadth and high spatial resolution, that multitaxonomic rather than single-taxon approaches are critical for identifying areas likely to promote the persistence of most species. Our conservation prioritization, facilitated by newly available techniques, identifies optimal expansion sites for the Madagascar government's current goal of tripling the land area under protection. Our findings further suggest that high-resolution multitaxonomic approaches to prioritization may be necessary to ensure protection for biodiversity in other global hot spots. [ABSTRACT FROM AUTHOR]

Cytidine deaminases of the APOBEC3 family all have specificity for single-stranded DNA, which may become exposed during replication or transcription of double-stranded DNA. Three human APQBEC3A (hA3A), hA3B, and hA3H genes are expressed in keratinocytes and skin, leading us to determine whether genetic editing of human papillomavirus (HPV) DNA occurred. In a study of HPV1a plantar warts and HPV16 precancerous cervical biopsies, hyperedited HPV1a and HPV16 genomes were found. Strictly analogous results were obtained from transfection experiments with HPV plasmid DNA and the three nuclear localized enzymes: hA3A, hA3C, and hA3H. Thus, stochastic or transient overexpression of APOBEC3 genes may expose the genome to a broad spectrum of mutations that could influence the development of tumors. [ABSTRACT FROM AUTHOR]

AMPA glutamate receptors (AMPARs) mediate fast excitatory synaptic transmission. Upon fast consecutive synaptic stimulation, transmission can be depressed. Recuperation from fast synaptic depression has been attributed solely to recovery of transmitter release and/or AMPAR desensitization. We show that AMPAR lateral diffusion, observed in both intact hippocampi and cultured neurons, allows fast exchange of desensitized receptors with naïve functional ones within or near the postsynaptic density. Recovery from depression in the tens of millisecond time range can be explained in part by this fast receptor exchange. Preventing AMPAR surface movements through cross-linking, endogenous clustering, or calcium rise all slow recovery from depression. Physiological regulation of postsynaptic receptor mobility affects the fidelity of synaptic transmission by shaping the frequency dependence of synaptic responses. [ABSTRACT FROM AUTHOR]

The ability to select a better option from multiple acceptable ones is important for animals to optimize their resources. The mechanisms that underlie such decision-making processes are not well understood. We found that selection of egg-laying site in Drosophila melanogaster is a suitable system to probe the neural circuit that governs simple decision-making processes. First, Drosophila females pursue active probing of the environment before depositing each egg, apparently to evaluate site quality for every egg. Second, Drosophila females can either accept or reject a sucrose-containing medium, depending on the context. Last, communication of the "acceptability" of the sucrose-containing medium as an egg-laying option to the reproductive system depends on the function of a group of insulin-like peptide 7 (ILP7)-producing neurons. These findings suggest that selection of egg-laying site involves a simple decision-making process and provide an entry point toward a systematic dissection of this process. [ABSTRACT FROM AUTHOR]

Activation of cyclin-dependent kinase 1 (Cdk1) has been linked to cell death of postmitotic neurons in brain development and disease. We found that Cdk1 phosphorylated the transcription factor FOXO1 at Ser249 in vitro and in vivo. The phosphorylation of FOXO1 at Ser249 disrupted FOXO1 binding with 14-3-3 proteins and thereby promoted the nuclear accumulation of FOXO1 and stimulated FOXO1-dependent transcription, leading to cell death in neurons. In proliferating cells, Cdk1 induced FOXO1 Ser249 phosphorylation at the G2/M phase of the cell cycle, resulting in FOXO1-dependent expression of the mitotic regulator Polo-like kinase (Plk). These findings define a conserved signaling link between Cdk1 and FOXO1 that may have a key role in diverse biological processes, including the degeneration of postmitotic neurons. [ABSTRACT FROM AUTHOR]

Staphylococcus aureus is one of the most successful human pathogens, colonizing 2 billion individuals worldwide and causing invasive infections even in immunocompetent hosts. S. aureus can evade multiple components of host innate immunity, including the antimicrobial radical nitric oxide (NO•) produced by activated phagocytes. We show that S. aureus is capable of metabolically adapting to nitrosative stress by expressing an NO•-inducible L-lactate dehydrogenase (ldh1, SACOL0222) divergently transcribed from the NO•-detoxifying flavohemoglobin (hmp). L-Lactate production allows S. aureus to maintain redox homeostasis during nitrosative stress and is essential for virulence. NO•-inducible lactate dehydrogenase activity and NO• resistance distinguish S. aureus from the closely related commensal species S. epidermidis and S. saprophyticus. [ABSTRACT FROM AUTHOR]

Bipedalism is a key human adaptation and a defining feature of the hominin clade. Fossil femora discovered in Kenya and attributed to Orrorin tugenensis, at 6 million years ago, purportedly provide the earliest postcranial evidence of hominin bipedalism, but their functional and phylogenetic affinities are controversial. We show that the O. tugenensis femur differs from those of apes and Homo and most strongly resembles those of Australopithecus and Paranthropus, indicating that O. tugenensis was bipedal but is not more closely related to Homo than to Australopithecus. Femoral morphology indicates that O. tugenensis shared distinctive hip biomechanics with australopiths, suggesting that this complex evolved early in human evolution and persisted for almost 4 million years until modifications of the hip appeared in the late Pliocene in early Homo. [ABSTRACT FROM AUTHOR]

Mouse CD4+CD8+ double-positive (DP) thymocytes differentiate into CD4+ helper-lineage cells upon expression of the transcription factor Th-POK but commit to the CD8+ cytotoxic lineage in its absence. We report the redirected differentiation of class I-restricted thymocytes into CD4+CD8 helper-like T cells upon loss of Runx transcription factor complexes. A Runx-binding sequence within the Th-POK locus acts as a transcriptional silencer that is essential for Th-POK repression and for development of CD8+ T cells. Thus, Th-POK expression and genetic programming for I helper cell development are actively inhibited by Runx-dependent silencer activity, allowing for cytotoxic T cell differentiation. Identification of the transcription factors network in CD4 and CD8 lineage choice provides insight into how distinct T cell subsets are developed for regulating the adaptive immune system. [ABSTRACT FROM AUTHOR]

Although commensalism with gut microbiota exists in all metazoans, the host factors that maintain this homeostatic relationship remain largely unknown. We show that the intestinal homeobox gene Caudal regulates the commensal-gut mutualism by repressing nuclear factor kappa B-dependent antimicrobial peptide genes. Inhibition of Caudal expression in flies via RNA interference led to overexpression of antimicrobial peptides, which in turn altered the commensal population within the intestine. In particular, the dominance of one gut microbe, Gluconobacter sp. strain EW707, eventually led to gut cell apoptosis and host mortality. However, restoration of a healthy microbiota community and normal host survival in the Caudal-RNAi flies was achieved by reintroduction of the Caudal gene. These results reveal that a specific genetic deficiency within a host can profoundly influence the gut commensal microbial community and host physiology. [ABSTRACT FROM AUTHOR]

Robotics researchers increasingly agree that ideas from biology and self-organization can strongly benefit the design of autonomous robots. Biological organisms have evolved to perform and survive in a world characterized by rapid changes, high uncertainty, indefinite richness, and limited availability of information. Industrial robots, in contrast, operate in highly controlled environments with no or very little uncertainty. Although many challenges remain, concepts from biologically inspired (bio-inspired) robotics will eventually enable researchers to engineer machines for the real world that possess at least some of the desirable properties of biological organisms, such as adaptivity, robustness, versatility, and agility. [ABSTRACT FROM AUTHOR]

Astrocytes play active roles in brain physiology. They respond to neurotransmitters and modulate neurona excitability and synaptic function. However, the influence of astrocytes on synaptic transmission and plasticity at the single synapse Level is unknown. Ca2+ elevation in astrocytes transiently increased the probability of transmitter release at hippocampal area CA3-CA1 synapses, without affecting the amplitude of synaptic events. This form of short-term plasticity was due to the release of glutamate from astrocytes, a process that depended on Ca2+ and soluble N-ethylmaleimide—sensitive factor attachment protein receptor (SNARE) protein and that activated metabotropic glutamate receptors (mGluRs). The transient potentiation of transmitter release became persistent when the astrocytic signal was temporally coincident with postsynaptic depolarization. This persistent plasticity was mGluR-mediated but N-methyl-o-aspartate receptor- independent. These results indicate that astrocytes are actively involved in the transfer and storage of synaptic information. [ABSTRACT FROM AUTHOR]

The genomes of individuals from the same species vary in sequence as a result of different evolutionary processes. To examine the patterns of, and the forces shaping, sequence variation in Arabidopsis thaliana, we performed high-density array resequencing of 20 diverse strains (accessions). More than 1 million nonredundant single-nucleotide polymorphisms (SNPs) were identified at moderate false discovery rates (FDRs), and ~4% of the genome was identified as being highly dissimilar or deleted relative to the reference genome sequence. Patterns of polymorphism are highly nonrandom among gene families, with genes mediating interaction with the biotic environment having exceptional polymorphism levels. At the chromosomal scale, regional variation in polymorphism was readily apparent. A scan for recent selective sweeps revealed several candidate regions, including a notable example in which almost all variation was removed in a 500-kilobase window. Analyzing the polymorphisms we describe in larger sets of accessions will enable a detailed understanding of forces shaping population-wide sequence variation in A. thaliana. [ABSTRACT FROM AUTHOR]

The biological cell is equipped with a variety of molecular machines that perform complex mechanical tasks such as cell division or intracellular transport. One can envision employing these biological motors in artificial environments. We review the progress that has been made in using motor proteins for powering or manipulating nanoscale components. In particular, kinesin and myosin biomotors that move along linear biofilaments have been widely explored as active components. Currently realized applications are merely proof-of-principle demonstrations. Yet, the sheer availability of an entire ready-to-use toolbox of nanosized biological motors is a great opportunity that calls for exploration. [ABSTRACT FROM AUTHOR]

A systematic fluorescence in situ hybridization comparison of macaque and human synteny organization disclosed five additional macaque evolutionary new centromeres (ENCs) for a total of nine ENCs. To understand the dynamics of ENC formation and progression, we compared the ENC of macaque chromosome 4 with the human orthologous region, at 6q24.3, that conserves the ancestral genomic organization. A 250-kilobase segment was extensively duplicated around the macaque centromere. These duplications were strictly intrachromosomal. Our results suggest that novel centromeres may trigger only local duplication activity and that the absence of genes in the seeding region may have been important in ENC maintenance and progression. [ABSTRACT FROM AUTHOR]

The article focuses on the development in the field of molecular genetics. According to the author, numerous tools have been developed recently that exploit breakthroughs in the cognition of genomic chemistries. From improved sequencing technologies to microRNA detection, advances in basic chemistry have been translated into viable products, which can help scientists in achieving their research and clinical goals. As cross-disciplinary communication continues to grow and mature, the author stresses, that research at the intersection of chemistry and biology is increasingly exploited to solve fundamental questions in science and medicine.

Toxoplasma gondii strains differ dramatically in virulence despite being genetically very similar. Genetic mapping revealed two closely adjacent quantitative trait loci on parasite chromosome Vlla that control the extreme virulence of the type I lineage. Positional cloning identified the candidate virulence gene ROP18, a highly polymorphic serine-threonine kinase that was secreted into the host cell during parasite invasion. Transfection of the virulent ROP18 allele into a nonpathogenic type III strain increased growth and enhanced mortality by 4 to 5 logs. These attributes of ROP18 required kinase activity, which revealed that secretion of effectors is a major component of parasite virulence. [ABSTRACT FROM AUTHOR]

Empathy is thought to be unique to higher primates, possibly to humans alone. We report the modulation of pain sensitivity in mice produced solely by exposure to their cagemates, but not to strangers, in pain. Mice tested in dyads and given an identical noxious stimulus displayed increased pain behaviors with statistically greater co-occurrence, effects dependent on visual observation. When familiar mice were given noxious stimuli of different intensities, their pain behavior was influenced by their neighbor's status bidirectionally. Finally, observation of a cagemate in pain altered pain sensitivity of an entirely different modality, suggesting that nociceptive mechanisms in general are sensitized. [ABSTRACT FROM AUTHOR]

During embryogenesis, stem cells are set aside to fuel the postnatal hair cycle and repair the epidermis after injury. To define how hair follicle stem cells are specified and maintained in an undifferentiated state, we developed a strategy to isolate and transcriptionally profile embryonic hair progenitors in mice. We identified Lhx2 as a transcription factor positioned downstream of signals necessary to specify hair follicle stem cells, but upstream from signals required to drive activated stem cells to terminally differentiate. Using gain- and loss-of-function studies, we uncovered a role for Lhx2 in maintaining the growth and undifferentiated properties of hair follicle progenitors. [ABSTRACT FROM AUTHOR]

Ecological interactions, such as predation and bioturbation, are thought to be fundamental determinants of macroevolutionary trends. A data set containing global occurrences of Phanerozoic fossils of benthic marine invertebrates shows escalatory trends in the relative frequency of ecological groups, such as carnivores and noncarnivorous infaunal or mobile organisms. Associations between these trends are either statistically insignificant or interpretable as preservational effects. Thus, there is no evidence that escalation drives macroecological trends at global and million-year time scales, We also find that taxonomic richness and occurrence data are cross-correlated, which justifies the traditional use of one as a proxy of the other. [ABSTRACT FROM AUTHOR]

We present a large-scale molecular phylogeny of the ants (Hymenoptera: Formicidae), based on 4.5 kilobases of sequence data from six gene regions extracted from 139 of the 288 described extant genera, representing 19 of the 20 subfamilies. All but two subfamilies are recovered as monophyletic. Divergence time estimates calibrated by minimum age constraints from 43 fossils indicate that most of the subfamilies representing extant ants arose much earlier than previously proposed but only began to diversify during the Late Cretaceous to Early Eocene. This period also witnessed the rise of angiosperms and most herbivorous insects. [ABSTRACT FROM AUTHOR]

We directly observed real-time production of single protein molecules in individual Escherichia coli cells. A fusion protein of a fast-maturing yellow fluorescent protein (YFP) and a membrane-targeting peptide was expressed under a repressed condition. The membrane-localized YFP can be detected with single-molecule sensitivity. We found that the protein molecules are produced in bursts, with each burst originating from a stochastically transcribed single messenger RNA molecule, and that protein copy numbers in the bursts follow a geometric distribution. The quantitative study of low-level gene expression demonstrates the potential of single-molecule experiments in elucidating the workings of fundamental biological processes in living cells. [ABSTRACT FROM AUTHOR]

Over the past 20 years, the technological impediments to fabricating electrodes of micrometer dimensions have been largely overcome. These small electrodes can be readily applied to probe chemical events at the surface of tissues or individual biological cells; they can even be used to monitor concentration changes within intact animals. These measurements can be made on rapid time scales and with minimal perturbation of the system under study. Several recent applications have provided important insights into chemical processes at cells and in tissues. Examples include molecular flux measurements at the surface of single cells and through skin — which can offer insights into oxidative stress, exocytosis, and drug delivery — and real-time brain neurotransmitter monitoring in living rats, which reveals correlations between behavior and molecular events in the brain. Such findings can promote interdisciplinary collaborations and may lead to a broader understanding of the chemical aspects of biology. [ABSTRACT FROM AUTHOR]

Mixing and transport in turbulent flows — which have strong local concentration fluctuations — are essential in many natural and industrial systems including reactions in chemical mixers, combustion in engines and burners, droplet formation in warm clouds, and biological odor detection and chemotaxis. Local concentration fluctuations, in turn, are intimately tied to the problem of the separation of pairs of fluid elements. We have measured this separation rate in an intensely turbulent laboratory flow and have found, in quantitative agreement with the seminal predictions of Batchelor, that the initial separation of the pair plays an important role in the subsequent spreading of the fluid elements. These results have surprising consequences for the decay of concentration fluctuations and have applications to biological and chemical systems. [ABSTRACT FROM AUTHOR]

Plants may "eavesdrop" on volatile organic compounds (VOCs) released by herbivore-attacked neighbors to activate defenses before being attacked themselves. Transcriptome and signal cascade analyses of VOC-exposed plants suggest that plants eavesdrop to prime direct and indirect defenses and to hone competitive abilities. Advances in research on VOC biosynthesis and perception have facilitated the production of plants that are genetically "deaf" to particular VOCs or "mute" in elements of their volatile vocabulary. Such plants, together with advances in VOC analytical instrumentation, will allow researchers to determine whether fluency enhances the fitness of plants in natural communities. [ABSTRACT FROM AUTHOR]

The article reports on the automation of biological laboratories. Genomics, proteomics, and systems biology have one key factor in common: They generate huge amounts of data. To handle that information reliably, life scientists turn to laboratory automation. In response to that demand, vendors now offer tools and technologies that appeal to both individual researchers new to the field and sophisticated users. Laboratory automation offers benefits beyond allowing scientists to carry out more tasks faster. People need to know that the results of research can be trusted. Laboratory automation enables that. Major points in modern life science are validation and data quality; legal validation, patents, and clinical testing have become crucial issues. Automation allows a much higher reproducibility of data and better documentation of the data, and allows to produce more data points more easily. The technology also has a role in potentially dangerous experimentation. Laboratory automation works at two levels: one involves robots and allows a group to process more samples; and the other increases throughput by permitting scientists to look at.

The cell lineages that form the transporting tissues (xylem and phloem) and the intervening pluripotent procambial tissue originate from stem cells near the root tip. We demonstrate that in Arabidopsis, cytokinin phytohormones negatively regulate protoxylem specification. AHP6, an inhibitory pseudophosphotransfer protein, counteracts cytokinin signaling, allowing protoxylem formation. Conversely, cytokinin signaling negatively regulates the spatial domain of AHP6 expression. Thus, by controlling the identity of cell lineages, the reciprocal interaction of cytokinin signaling and its spatially specific modulator regulates proliferation and differentiation of cell lineages during vascular development, demonstrating a previously unrecognized regulatory circuit underlying meristem organization. [ABSTRACT FROM AUTHOR]