The genome of Aiptasia,a sea anemone model for coral symbiosis

The most diverse marine ecosystems, coral reefs, depend upon a functional symbiosis between a cnidarian animal host (the coral) and intracellular photosynthetic dinoflagellate algae. The molecular and cellular mechanisms underlying this endosymbiosis are not well understood, in part because of the difficulties of experimental work with corals. The small sea anemone Aiptasia provides a tractable laboratory model for investigating these mechanisms. Here we report on the assembly and analysis of the Aiptasia genome, which will provide a foundation for future studies and has revealed several features that may be key to understanding the evolution and function of the endosymbiosis. These features include genomic rearrangements and taxonomically restricted genes that may be functionally related to the symbiosis, aspects of host dependence on alga-derived nutrients, a novel and expanded cnidarian-specific family of putative pattern-recognition receptors that might be involved in the animal–algal interactions, and extensive lineage-specific horizontal gene transfer. Extensive integration of genes of prokaryotic origin, including genes for antimicrobial peptides, presumably reflects an intimate association of the animal–algal pair also with its prokaryotic microbiome.Coral reefs form marine-biodiversity hotspots that are of enormous ecological, economic, and aesthetic importance. Coral growth and reef deposition are based energetically on the endosymbiosis between the cnidarian animal hosts and photosynthetic dinoflagellate algae of the genus Symbiodinium, which live in vesicles within the gastrodermal (gut) cells of the animal and typically supply ≥90% of its total energy, while the host provides the algae with a sheltered environment and the inorganic nutrients needed for photosynthesis and growth (1). This tight metabolic coupling allows the holobiont (i.e., the animal host and its microbial symbionts) to thrive in nutrient-poor waters. Although the ecology of coral reefs has been studied intensively, the molecular and cellular mechanisms underlying the critical endosymbiosis remain poorly understood (2). As coral reefs face an ongoing and increasing threat from anthropogenic environmental change (3), new insights into these mechanisms are of critical importance to understanding the resilience and adaptability of coral reefs and thus to the planning of conservation strategies (4).Aiptasia is a globally distributed sea anemone that harbors endosymbiotic Symbiodinium like its Class Anthozoa relatives the stony corals (Fig. 1 and SI Appendix, Fig. S1A) (4, 5). Aiptasia has a range of polyp sizes convenient for experimentation and is easily grown in laboratory culture, where it reproduces both asexually (so that large clonal populations can be obtained) and sexually (allowing experiments on larvae and potentially genetic studies), and it can be maintained indefinitely in an aposymbiotic (dinoflagellate-free) state and reinfected by a variety of Symbiodinium strains (6, 7). These characteristics make Aiptasia a highly attractive model system for studies of the molecular and cellular basis of the cnidarian–dinoflagellate endosymbiosis (2, 4). To provide a solid platform for research on Aiptasia, we have sequenced and analyzed its genome. The results have already provided important insights into several aspects of the evolution and function of the symbiotic system.Open in a separate windowFig. 1.Phylogenetic position and different symbiotic states of Aiptasia. (A) Partial phylogenetic tree (see SI Appendix, SI Materials and Methods and Fig. S1A for details) shows Aiptasia grouped with other anthozoans among the cnidarians. Numbers on nodes denote bootstrap values. (B–D) An aposymbiotic Aiptasia polyp (B) and symbiotic polyps viewed under white light (C) or by fluorescence microscopy to visualize the red chlorophyll autofluorescence of the endosymbiotic Symbiodinium algae (D).     

Redesigning photosynthesis to sustainably meet global food and bioenergy demand

The world’s crop productivity is stagnating whereas population growth, rising affluence, and mandates for biofuels put increasing demands on agriculture. Meanwhile, demand for increasing cropland competes with equally crucial global sustainability and environmental protection needs. Addressing this looming agricultural crisis will be one of our greatest scientific challenges in the coming decades, and success will require substantial improvements at many levels. We assert that increasing the efficiency and productivity of photosynthesis in crop plants will be essential if this grand challenge is to be met. Here, we explore an array of prospective redesigns of plant systems at various scales, all aimed at increasing crop yields through improved photosynthetic efficiency and performance. Prospects range from straightforward alterations, already supported by preliminary evidence of feasibility, to substantial redesigns that are currently only conceptual, but that may be enabled by new developments in synthetic biology. Although some proposed redesigns are certain to face obstacles that will require alternate routes, the efforts should lead to new discoveries and technical advances with important impacts on the global problem of crop productivity and bioenergy production.     

From the Cover: Dietary changes of large herbivores in the Turkana Basin,Kenya from 4 to 1 Ma

A large stable isotope dataset from East and Central Africa from ca. 30 regional collection sites that range from forest to grassland shows that most extant East and Central African large herbivore taxa have diets dominated by C₄ grazing or C₃ browsing. Comparison with the fossil record shows that faunal assemblages from ca. 4.1–2.35 Ma in the Turkana Basin had a greater diversity of C₃–C₄ mixed feeding taxa than is presently found in modern East and Central African environments. In contrast, the period from 2.35 to 1.0 Ma had more C₄-grazing taxa, especially nonruminant C₄-grazing taxa, than are found in modern environments in East and Central Africa. Many nonbovid C₄ grazers became extinct in Africa, notably the suid Notochoerus, the hipparion equid Eurygnathohippus, the giraffid Sivatherium, and the elephantid Elephas. Other important nonruminant C₄-grazing taxa switched to browsing, including suids in the lineage Kolpochoerus-Hylochoerus and the elephant Loxodonta. Many modern herbivore taxa in Africa have diets that differ significantly from their fossil relatives. Elephants and tragelaphin bovids are two groups often used for paleoecological insight, yet their fossil diets were very different from their modern closest relatives; therefore, their taxonomic presence in a fossil assemblage does not indicate they had a similar ecological function in the past as they do at present. Overall, we find ecological assemblages of C₃-browsing, C₃–C₄-mixed feeding, and C₄-grazing taxa in the Turkana Basin fossil record that are different from any modern ecosystem in East or Central Africa.The expansion of C₄ biomass beginning in the late Miocene marks a major vegetation change in the history of Earth. Today C₄ plants comprise ca. 50% of net primary productivity (NPP) in the tropics (1) yet contributed less than 1% of NPP only 10 million years ago. C₄ plants are primarily grasses and sedges, although C₄ photosynthesis is known to be used in ∼20 plant families (2, 3). C₄ photosynthesis is an adaptation to low (ca. <500 ppm by volume) concentrations of CO₂ in Earth’s atmosphere along with high growing-season temperatures (4). Although genetic evidence indicates an Oligocene origin of C₄ photosynthesis in the grasses (5, 6), macrofossil evidence for C₄ photosynthesis in grasses is extremely sparse (7, 8).The expansion of C₄ biomass has been documented through stable isotopes in paleosols (9–12), grass phytoliths (13), herbivore tooth enamel (14–16), and biomarkers in deep-sea sediments (17, 18). At 10 Ma in Africa, Asia, and North America, the δ¹³C values for equid tooth enamel indicate a diet dominated by C₃ vegetation; by ca. 7 Ma, equids in Africa have a diet dominated (>75%) by C₄ vegetation (14, 15). In East Africa today there is a distinct difference in diets of major herbivores, with most mammals either being predominantly browsing (>ca. 75% C₃) or grazing (>ca. 75% C₄), and there are relatively few mixed feeders (Fig. 1).Open in a separate windowFig. 1.δ¹³C₁₇₅₀ values for tooth enamel (or equivalent) for >1,900 mammals from East and Central Africa (principal localities in SI Appendix, Table S1; data from Dataset S1).A recent study of the early transition of C₃ to C₄ dietary change in the Turkana Basin from 10 Ma to ca. 4 Ma (15) showed that equids were the earliest mammals to fully exploit the C₄ dietary resource, attaining a predominantly C₄-grazing diet by 7 Ma. Other mammal groups (hippopotamids, elephantids, and bovids) changed to a C₄ diet later than did the equids. In this paper we document dietary changes in the major Artiodactyla-Perissodactyla-Proboscidea (APP) taxa in the Turkana Basin between ca. 4 Ma and 1 Ma and compare those to dietary preferences of extant APP taxa in East and Central Africa. The Turkana Basin has an excellent stratigraphy (19–22) with excellent preservation of fossils from 4 to 1 Ma; this study focuses on fossils recovered from the Koobi Fora, Kanapoi, and Nachukui Formations of northern Kenya.We compare dietary changes within the major APP taxa through the past 4 Ma in the formations listed above using >900 individual fossils that represent the major taxa collected within the principal stratigraphic intervals of these formations. Fossil mammalian diets are compared with those of >1,900 extant mammal individuals sampled from >30 different regions and habitats in eastern and central Africa. We compare the ecosystem structure (C₃ browsers, C₃/C₄ mixed diets, and C₄ grazers) through the Pliocene and Pleistocene and document changes in ungulate diets over time.     

Gradient Spin Echo (GraSE) imaging for fast myocardial T2 mapping

Background

Quantitative Cardiovascular Magnetic Resonance (CMR) techniques have gained high interest in CMR research. Myocardial T2 mapping is thought to be helpful in diagnosis of acute myocardial conditions associated with myocardial edema. In this study we aimed to establish a technique for myocardial T2 mapping based on gradient-spin-echo (GraSE) imaging.

Methods

The local ethics committee approved this prospective study. Written informed consent was obtained from all subjects prior to CMR. A modified GraSE sequence allowing for myocardial T2 mapping in a single breath-hold per slice using ECG-triggered acquisition of a black blood multi-echo series was developed at 1.5 Tesla. Myocardial T2 relaxation time (T2-RT) was determined by maximum likelihood estimation from magnitude phased-array multi-echo data. Four GraSE sequence variants with varying number of acquired echoes and resolution were evaluated in-vitro and in 20 healthy volunteers. Inter-study reproducibility was assessed in a subset of five volunteers. The sequence with the best overall performance was further evaluated by assessment of intra- and inter-observer agreement in all volunteers, and then implemented into the clinical CMR protocol of five patients with acute myocardial injury (myocarditis, takotsubo cardiomyopathy and myocardial infarction).

Results

In-vitro studies revealed the need for well defined sequence settings to obtain accurate T2-RT measurements with GraSE. An optimized 6-echo GraSE sequence yielded an excellent agreement with the gold standard Carr-Purcell-Meiboom-Gill sequence. Global myocardial T2 relaxation times in healthy volunteers was 52.2 ± 2.0 ms (mean ± standard deviation). Mean difference between repeated examinations (n = 5) was −0.02 ms with 95% limits of agreement (LoA) of [−4.7; 4.7] ms. Intra-reader and inter-reader agreement was excellent with mean differences of −0.1 ms, 95% LoA = [−1.3; 1.2] ms and 0.1 ms, 95% LoA = [−1.5; 1.6] ms, respectively (n = 20). In patients with acute myocardial injury global myocardial T2-RTs were prolonged (mean: 61.3 ± 6.7 ms).

Conclusion

Using an optimized GraSE sequence CMR allows for robust, reliable, fast myocardial T2 mapping and quantitative tissue characterization. Clinically, the GraSE-based T2-mapping has the potential to complement qualitative CMR in patients with acute myocardial injuries.

Electronic supplementary material

The online version of this article (doi:10.1186/s12968-015-0127-z) contains supplementary material, which is available to authorized users.     

Dicer is required for chromosome segregation and gene silencing in fission yeast cells

RNA interference is a form of gene silencing in which the nuclease Dicer cleaves double-stranded RNA into small interfering RNAs. Here we report a role for Dicer in chromosome segregation of fission yeast. Deletion of the Dicer (dcr1+) gene caused slow growth, sensitivity to thiabendazole, lagging chromosomes during anaphase, and abrogated silencing of centromeric repeats. As Dicer in other species, Dcr1p degraded double-stranded RNA into approximately 23 nucleotide fragments in vitro, and dcr1Delta cells were partially rescued by expression of human Dicer, indicating evolutionarily conserved functions. Expression profiling demonstrated that dcr1+ was required for silencing of two genes containing a conserved motif.     

In vivo characterization of chronic traumatic encephalopathy using [F-18]FDDNP PET brain imaging

Chronic traumatic encephalopathy (CTE) is an acquired primary tauopathy with a variety of cognitive, behavioral, and motor symptoms linked to cumulative brain damage sustained from single, episodic, or repetitive traumatic brain injury (TBI). No definitive clinical diagnosis for this condition exists. In this work, we used [F-18]FDDNP PET to detect brain patterns of neuropathology distribution in retired professional American football players with suspected CTE (n = 14) and compared results with those of cognitively intact controls (n = 28) and patients with Alzheimer’s dementia (AD) (n = 24), a disease that has been cognitively associated with CTE. [F-18]FDDNP PET imaging results in the retired players suggested the presence of neuropathological patterns consistent with models of concussion wherein brainstem white matter tracts undergo early axonal damage and cumulative axonal injuries along subcortical, limbic, and cortical brain circuitries supporting mood, emotions, and behavior. This deposition pattern is distinctively different from the progressive pattern of neuropathology [paired helical filament (PHF)-tau and amyloid-β] in AD, which typically begins in the medial temporal lobe progressing along the cortical default mode network, with no or minimal involvement of subcortical structures. This particular [F-18]FDDNP PET imaging pattern in cases of suspected CTE also is primarily consistent with PHF-tau distribution observed at autopsy in subjects with a history of mild TBI and autopsy-confirmed diagnosis of CTE.The consensus statement on concussions from the Fourth International Conference on Concussion in Sports (Zurich 2012) (1) defines acute mild traumatic brain injury (mTBI) or cerebral concussion as a brain injury with a complex pathophysiological process induced by biomechanical forces. Cerebral concussion causes white matter axonal injury due to axonal shearing and stretching (2), typically resulting in the rapid onset of short-lived impairment of neurological function that resolves spontaneously and largely reflects a functional disturbance rather than a structural injury. As such, no abnormality is seen on standard structural neuroimaging determinations (1).A number of early literature reports described a neurodegenerative disease associated with a history of repetitive TBI in retired professional boxers (3, 4), with a prevalence rate of up to 47% among retired professional boxers aged 50 y and older who boxed for more than 10 y (5). Initially named “punch drunk syndrome” (3) and dementia pugilistica (4), this syndrome is now known as chronic traumatic encephalopathy (CTE) in the current literature (6, 7).Compelling autopsy evidence (6–8) and neurobehavioral determinations (9) of retired professional American football athletes indicate that a subgroup develops neurodegenerative and clinical changes typical of CTE, a progressive syndrome distinctively different from Alzheimer’s disease (AD), which is the most common form of dementia in the elderly (10). The connection between multiple concussions and subconcussive head impacts (2) and CTE is compelling, because history of repetitive concussions is the strongest risk factor for development of CTE in numerous contact sports (e.g., American football, rugby, boxing, ice hockey, soccer, and professional wrestling), in war veterans with a history of blast or blunt force TBI, and in conditions where trauma to the head occurs for various reasons (e.g., falls during seizures, head-banging in autistic children, motor vehicle and domestic accidents, domestic violence and abuse) (6, 8, 11–14). As with most neurodegenerative diseases, clinical diagnosis remains elusive due to the lack of specificity of CTE clinical symptomatology criteria, and histopathological examination of brain at autopsy is the most definitive diagnostic modality (6, 8, 11).The novel imaging approaches leading to the in vivo characterization of CTE brain neuropathology premortem (e.g., PET) are complementary to structural imaging modalities [e.g., diffusion tensor imaging MRI (DTI MRI)] and offer a specific and sensitive strategy to facilitate diagnosis of CTE. Neuronal and glial fibrillar hyperphosphorylated microtubule-associated protein tau deposits composed of paired helical filament (PHF)-tau are the primary brain proteinopathy of CTE based on autopsy determinations, and their 3R/4R tau isoform ratio is similar to that of AD (11). Their topographically predictable pattern of distribution was used as a basis for a severity staging system of CTE neuropathology (7), ranging from mild (neuropathology stages I and II) to advanced (neuropathology stages III and IV) (7) (Tables S1 and S2). In addition, more than 80% of analyzed pathologically confirmed CTE cases also show transactive response (TAR) DNA-binding protein of ∼43 kDa (TDP-43) either as inclusions in sparse neurites in cortex, medial temporal lobe structures, and brainstem in CTE neuropathology stages I–III, as widespread neuronal and glial inclusions in severe CTE cases (neuropathology stage IV), or in CTE cases with motor neuron disease (7, 15) (Tables S1 and S2). CTE cases also can exhibit the presence of other fibrillar protein aggregates. McKee et al. (7) and Omalu et al. (8) reported that in autopsy determinations, less than half of all CTE cases and less than one third of “pure” CTE cases show amyloid-β (Aβ) deposits, predominantly as scattered cortical diffuse plaques in low density (Tables S1 and S2). Of note is that subjects with Aβ deposits were significantly older than those without. Moreover, their neuropathology was more severe than that in cases without Aβ deposits and was often combined with α-synuclein deposits (7). As an example, as reported by McKee et al. (7), of 30 CTE cases with at least some cortical Aβ deposits (of 68 confirmed CTE cases), 29 brains were from subjects who died in their seventh decade of life and one from a subject who died in his sixth decade.Subsequent to our preliminary report (16), in this work we use [F-18]FDDNP, an imaging agent for fibrillar insoluble protein aggregates (16–20), and PET imaging with the aim of establishing (i) topographic brain localization of [F-18]FDDNP PET signals indicative of fibrillar neuroaggregates in retired professional American football players with suspected CTE (mTBI group) vs. controls (CTRL); (ii) determination of [F-18]FDDNP PET signal patterns in the mTBI group; (iii) presence of [F-18]FDDNP PET signal as a measure of neuropathology in the brain areas involved in mood disorders related neurocircuits; (iv) correlation of [F-18]FDDNP PET results with neuropathology distributions in confirmed CTE cases; (v) differential patterns of [F-18]FDDNP PET signals, and thus deposition of fibrillar neuroaggregates, in the mTBI group with respect to the AD group; and (vi) preliminary demonstration of differences in [F-18]FDDNP PET signal patterns in mTBI cases with different etiology, i.e., contact-sport–related mTBI in retired professional American football players vs. blast-induced mTBI in war veterans. We further intended to demonstrate that tau (vs. Aβ) specificity of high affinity PET molecular imaging probes may not be a necessary requirement when used in CTE subjects with primary proteinopathy in the form of PHF-tau (8): PET imaging probes potentially sensitive to TDP-43 aggregates and Aβ deposits, which are present in higher densities almost exclusively in older CTE cases with more advanced neuropathology (e.g., stage IV), could better define disease progression based on quantification of differences in regional loads of combined neuropathologies because additional neuropathologies appear in predictable topographical and temporal patterns.