The genome sequence of the leaf-cutter ant Atta cephalotes reveals insights into its obligate symbiotic lifestyle

Leaf-cutter ants are one of the most important herbivorous insects in the Neotropics, harvesting vast quantities of fresh leaf material. The ants use leaves to cultivate a fungus that serves as the colony's primary food source. This obligate ant-fungus mutualism is one of the few occurrences of farming by non-humans and likely facilitated the formation of their massive colonies. Mature leaf-cutter ant colonies contain millions of workers ranging in size from small garden tenders to large soldiers, resulting in one of the most complex polymorphic caste systems within ants. To begin uncovering the genomic underpinnings of this system, we sequenced the genome of Atta cephalotes using 454 pyrosequencing. One prediction from this ant's lifestyle is that it has undergone genetic modifications that reflect its obligate dependence on the fungus for nutrients. Analysis of this genome sequence is consistent with this hypothesis, as we find evidence for reductions in genes related to nutrient acquisition. These include extensive reductions in serine proteases (which are likely unnecessary because proteolysis is not a primary mechanism used to process nutrients obtained from the fungus), a loss of genes involved in arginine biosynthesis (suggesting that this amino acid is obtained from the fungus), and the absence of a hexamerin (which sequesters amino acids during larval development in other insects). Following recent reports of genome sequences from other insects that engage in symbioses with beneficial microbes, the A. cephalotes genome provides new insights into the symbiotic lifestyle of this ant and advances our understanding of host-microbe symbioses.     

Compensatory T cell responses in IRG-deficient mice prevent sustained Chlamydia trachomatis infections

The obligate intracellular pathogen Chlamydia trachomatis is the most common cause of bacterial sexually transmitted diseases in the United States. In women C. trachomatis can establish persistent genital infections that lead to pelvic inflammatory disease and sterility. In contrast to natural infections in humans, experimentally induced infections with C. trachomatis in mice are rapidly cleared. The cytokine interferon-γ (IFNγ) plays a critical role in the clearance of C. trachomatis infections in mice. Because IFNγ induces an antimicrobial defense system in mice but not in humans that is composed of a large family of Immunity Related GTPases (IRGs), we questioned whether mice deficient in IRG immunity would develop persistent infections with C. trachomatis as observed in human patients. We found that IRG-deficient Irgm1/m3((-/-)) mice transiently develop high bacterial burden post intrauterine infection, but subsequently clear the infection more efficiently than wildtype mice. We show that the delayed but highly effective clearance of intrauterine C. trachomatis infections in Irgm1/m3((-/-)) mice is dependent on an exacerbated CD4(+) T cell response. These findings indicate that the absence of the predominant murine innate effector mechanism restricting C. trachomatis growth inside epithelial cells results in a compensatory adaptive immune response, which is at least in part driven by CD4(+) T cells and prevents the establishment of a persistent infection in mice.     

Micro-spatial genetic structure in song sparrows (<Emphasis Type="Italic">Melospiza melodia</Emphasis>)

The spatial genetic structure of populations is strongly influenced by current and historical patterns of gene flow and drift, which in the simplest case, is limited by geographic distance. We examined the microspatial genetic structure within 33 populations of song sparrows (Melospiza melodia) which included eight subspecies located across coastal areas in southern British Columbia (BC) and California. We also examined the effect of water barriers and local density estimates on genetic structuring. Across both regions, positive genetic structure was detectable at distances of less than 10 km. Genetic divergence was highest in Californian subspecies, perhaps due to reduced gene flow across sub-specific contact zones. In BC, populations distributed across islands displayed greater genetic structuring over similar spatial scales than those across mainland sites, supporting the prediction that water barriers reduce gene flow in this species. Our results confirm both the expectation for fine-scale genetic structure in these generally sedentary subspecies, and the role of landscape features in generating geographic variation in genetic structure.     

Prion diseases of yeast: amyloid structure and biology

Prion "variants" or "strains" are prions with the identical protein sequence, but different characteristics of the prion infection: e.g. different incubation periods for scrapie strains or different phenotype intensities for yeast prion variants. We have shown that infectious amyloids of the yeast prions [PSI+], [URE3] and [PIN+] each have an in-register parallel β-sheet architecture. Moreover, we have pointed out that this amyloid architecture can explain how one protein can faithfully transmit any of several conformations to new protein monomers. This explains how proteins can be genes.     

The dazed and confused identity of Agassiz's land tortoise, Gopherus agassizii (Testudines, Testudinidae) with the description of a new species, and its consequences for conservation

We investigate a cornucopia of problems associated with the identity of the desert tortoise, Gopherus agassizii (Cooper). The date of publication is found to be 1861, rather than 1863. Only one of the three original cotypes exists, and it is designated as the lectotype of the species. Another cotype is found to have been destroyed in the 1906 San Francisco earthquake and subsequent fire. The third is lost. The lectotype is genetically confirmed to be from California, and not Arizona, USA as sometimes reported. Maternally, the holotype of Gopherus lepidocephalus (Ottley & Velázques Solis. 1989) from the Cape Region of Baja California Sur, Mexico is also from the Mojavian population of the desert tortoise, and not from Tiburon Island, Sonora, Mexico as previously proposed. A suite of characters serve to diagnose tortoises west and north of the Colorado River, the Mojavian population, from those east and south of the river in Arizona, USA, and Sonora and Sinaloa, Mexico, the Sonoran population. Species recognition is warranted and because Gopherus lepidocephalus is from the Mojavian population, no names are available for the Sonoran species. Thus, a new species, Gopherus morafkaisp. n., is named and this action reduces the distribution of Gopherus agassizii to only 30% of its former range. This reduction has important implications for the conservation and protection of Gopherus agassizii, which may deserve a higher level of protection.     

Do invasive species show higher phenotypic plasticity than native species and,if so,is it adaptive? A meta‐analysis

Do invasive plant species have greater phenotypic plasticity than non-invasive species? And, if so, how does this affect their fitness relative to native, non-invasive species? What role might this play in plant invasions? To answer these long-standing questions, we conducted a meta-analysis using data from 75 invasive/non-invasive species pairs. Our analysis shows that invasive species demonstrate significantly higher phenotypic plasticity than non-invasive species. To examine the adaptive benefit of this plasticity, we plotted fitness proxies against measures of plasticity in several growth, morphological and physiological traits to test whether greater plasticity is associated with an improvement in estimated fitness. Invasive species were nearly always more plastic in their response to greater resource availability than non-invasives but this plasticity was only sometimes associated with a fitness benefit. Intriguingly, non-invasive species maintained greater fitness homoeostasis when comparing growth between low and average resource availability. Our finding that invasive species are more plastic in a variety of traits but that non-invasive species respond just as well, if not better, when resources are limiting, has interesting implications for predicting responses to global change.     

Plant traits and extinction in urban areas: a meta‐analysis of 11 cities

Aim Urban environments around the world share many features in common, including the local extinction of native plant species. We tested the hypothesis that similarity in environmental conditions among urban areas should select for plant species with a particular suite of traits suited to those conditions, and lead to the selective extinction of species lacking those traits. Location Eleven cities with data on the plant species that persisted and those that went locally extinct within at least the last 100 years following urbanization. Methods We compiled data on 11 plant traits for 8269 native species in the 11 cities and used hierarchical logistic regression models to identify the degree to which traits could distinguish species that persisted from those that went locally extinct in each city. The trait effects from each city were then combined in a meta‐analysis. Results The cities fell into two groups: those with relatively low rates of extinction (less than 0.05% species per year – Adelaide, Hong Kong, Los Angeles, San Diego and San Francisco), for which no traits reliably predicted the pattern of extinction, and those with higher rates of extinction (> 0.08% species per year – Auckland, Chicago, Melbourne, New York, Singapore and Worcester, MA), where short‐statured, small‐seeded plants were more likely to go extinct. Main conclusions Our analysis reveals patterns in trait selectivity consistent with local studies, suggesting some consistency in trait selection by urbanization. Overall, however, few traits reliably predicted the pattern of plant extinction across cities, making it difficult to identify a priori the extinction‐prone species most likely to be affected by urban expansion.     

An Investigation of the Effects of Sports-related Concussion in Youth Using Functional Magnetic Resonance Imaging and the Head Impact Telemetry System

One of the most commonly reported injuries in children who participate in sports is concussion or mild traumatic brain injury (mTBI)¹. Children and youth involved in organized sports such as competitive hockey are nearly six times more likely to suffer a severe concussion compared to children involved in other leisure physical activities². While the most common cognitive sequelae of mTBI appear similar for children and adults, the recovery profile and breadth of consequences in children remains largely unknown², as does the influence of pre-injury characteristics (e.g. gender) and injury details (e.g. magnitude and direction of impact) on long-term outcomes. Competitive sports, such as hockey, allow the rare opportunity to utilize a pre-post design to obtain pre-injury data before concussion occurs on youth characteristics and functioning and to relate this to outcome following injury. Our primary goals are to refine pediatric concussion diagnosis and management based on research evidence that is specific to children and youth. To do this we use new, multi-modal and integrative approaches that will:1.Evaluate the immediate effects of head trauma in youth 2.Monitor the resolution of post-concussion symptoms (PCS) and cognitive performance during recovery 3.Utilize new methods to verify brain injury and recoveryTo achieve our goals, we have implemented the Head Impact Telemetry (HIT) System. (Simbex; Lebanon, NH, USA). This system equips commercially available Easton S9 hockey helmets (Easton-Bell Sports; Van Nuys, CA, USA) with single-axis accelerometers designed to measure real-time head accelerations during contact sport participation ^{3 - 5}. By using telemetric technology, the magnitude of acceleration and location of all head impacts during sport participation can be objectively detected and recorded. We also use functional magnetic resonance imaging (fMRI) to localize and assess changes in neural activity specifically in the medial temporal and frontal lobes during the performance of cognitive tasks, since those are the cerebral regions most sensitive to concussive head injury ⁶. Finally, we are acquiring structural imaging data sensitive to damage in brain white matter.Download video file.^{(44M, mov)}     

Subcutaneous Administration of Muscarinic Antagonists and Triple-Immunostaining of the Levator Auris Longus Muscle in Mice

Hind limb muscles of rodents, such as gastrocnemius and tibialis anterior, are frequently used for in vivo pharmacological studies of the signals essential for the formation and maintenance of mammalian NMJs. However, drug penetration into these muscles after subcutaneous or intramuscular administration is often incomplete or uneven and many NMJs can remain unaffected. Although systemic administration with devices such as mini-pumps can improve the spatiotemporal effects, the invasive nature of this approach can cause confounding inflammatory responses and/or direct muscle damage. Moreover, complete analysis of the NMJs in a hind limb muscle is challenging because it requires time-consuming serial sectioning and extensive immunostaining. The mouse LAL is a thin, flat sheet of muscle located superficially on the dorsum of the neck. It is a fast-twitch muscle that functions to move the pinna. It contains rostral and caudal portions that originate from the midline of the cranium and extend laterally to the cartilaginous portion of each pinna. The muscle is supplied by a branch of the facial nerve that projects caudally as it exits the stylomastoid foramen. We and others have found LAL to be a convenient preparation that offers advantages for the investigation of both short and long-term in vivo effects of drugs on NMJs and muscles. First, its superficial location facilitates multiple local applications of drugs under light anesthesia. Second, its thinness (2-3 layers of muscle fibers) permits visualization and analysis of almost all the NMJs within the muscle. Third, the ease of dissecting it with its nerve intact together with the pattern of its innervation permits supplementary electrophysiological analysis in vitro^9,5. Last, and perhaps most importantly, a small applied volume (˜50μl) easily covers the entire muscle surface, provides a uniform and prolonged exposure of all its NMJs to the drug and eliminates the need for a systemic approach^1,8.Download video file.^{(45M, mov)}     

Complete genome sequence of Bacteroides helcogenes type strain (P 36-108)

Bacteroides helcogenes Benno et al. 1983 is of interest because of its isolated phylogenetic location and, although it has been found in pig feces and is known to be pathogenic for pigs, occurrence of this bacterium is rare and it does not cause significant damage in intensive animal husbandry. The genome of B. helcogenes P 36-108(T) is already the fifth completed and published type strain genome from the genus Bacteroides in the family Bacteroidaceae. The 3,998,906 bp long genome with its 3,353 protein-coding and 83 RNA genes consists of one circular chromosome and is a part of the Genomic Encyclopedia of Bacteria and Archaea project.