Site-selection model for optimal transplantation of eelgrass Zostera marina in the northeastern US

A site-selection model for eelgrass Zostera marina L. ecosystem restoration was developed in the northeastern US to select optimal areas for transplanting eelgrass. The site-selection model synthesizes available historic and literature-based information, reference data, and simple field measurements to identify and prioritize locations for large-scale eelgrass transplantation. Model development was based on the physical and biological characteristics associated with the most successful transplant sites in a mitigation project for the New Hampshire Port Authority. The site-selection process is divided into 3 phases: (1) the first phase uses available environmental information to formulate a preliminary transplant suitability index (PTSI) for pre-screening and eliminating unsuitable sites; (2) the second phase involves field measurements of light availability and bioturbation as well as survival and growth of test transplants at priority sites identified by the PTSI; (3) a transplant suitability index (TSI) score is calculated for each site based on the PTSI and the results of field assessments. The TSI is a multiplicative index that eliminates sites which receive ratings of zero and gives high scores to those sites with the greatest potential for successful transplantation. We applied the TSI post hoc to the New Hampshire Port Project¹s eelgrass transplant sites, and subsequently the site-selection model was used in an eelgrass restoration project in New Bedford Harbor, Massachusetts. After 2 yr of transplanting, the New Bedford Harbor effort has resulted in success at 62% of the sites planted using the site-selection model

HIV-1 RNA genome dimerizes on the plasma membrane in the presence of Gag protein

Retroviruses package a dimeric genome comprising two copies of the viral RNA. Each RNA contains all of the genetic information for viral replication. Packaging a dimeric genome allows the recovery of genetic information from damaged RNA genomes during DNA synthesis and promotes frequent recombination to increase diversity in the viral population. Therefore, the strategy of packaging dimeric RNA affects viral replication and viral evolution. Although its biological importance is appreciated, very little is known about the genome dimerization process. HIV-1 RNA genomes dimerize before packaging into virions, and RNA interacts with the viral structural protein Gag in the cytoplasm. Thus, it is often hypothesized that RNAs dimerize in the cytoplasm and the RNA-Gag complex is transported to the plasma membrane for virus assembly. In this report, we tagged HIV-1 RNAs with fluorescent proteins, via interactions of RNA-binding proteins and motifs in the RNA genomes, and studied their behavior at the plasma membrane by using total internal reflection fluorescence microscopy. We showed that HIV-1 RNAs dimerize not in the cytoplasm but on the plasma membrane. Dynamic interactions occur among HIV-1 RNAs, and stabilization of the RNA dimer requires Gag protein. Dimerization often occurs at an early stage of the virus assembly process. Furthermore, the dimerization process is probably mediated by the interactions of two RNA-Gag complexes, rather than two RNAs. These findings advance the current understanding of HIV-1 assembly and reveal important insights into viral replication mechanisms

SEQADAPT: an adaptable system for the tracking, storage and analysis of high throughput sequencing experiments

<p>Abstract</p> <p>Background</p> <p>High throughput sequencing has become an increasingly important tool for biological research. However, the existing software systems for managing and processing these data have not provided the flexible infrastructure that research requires.</p> <p>Results</p> <p>Existing software solutions provide static and well-established algorithms in a restrictive package. However as high throughput sequencing is a rapidly evolving field, such static approaches lack the ability to readily adopt the latest advances and techniques which are often required by researchers. We have used a loosely coupled, service-oriented infrastructure to develop SeqAdapt. This system streamlines data management and allows for rapid integration of novel algorithms. Our approach also allows computational biologists to focus on developing and applying new methods instead of writing boilerplate infrastructure code.</p> <p>Conclusion</p> <p>The system is based around the Addama service architecture and is available at our website as a demonstration web application, an installable single download and as a collection of individual customizable services.</p

Implementing Fault-tolerant Entangling Gates on the Five-qubit Code and the Color Code

We compare two different implementations of fault-tolerant entangling gates on logical qubits. In one instance, a twelve-qubit trapped-ion quantum computer is used to implement a non-transversal logical CNOT gate between two five qubit codes. The operation is evaluated with varying degrees of fault tolerance, which are provided by including quantum error correction circuit primitives known as flagging and pieceable fault tolerance. In the second instance, a twenty-qubit trapped-ion quantum computer is used to implement a transversal logical CNOT gate on two [[7,1,3]] color codes. The two codes were implemented on different but similar devices, and in both instances, all of the quantum error correction primitives, including the determination of corrections via decoding, are implemented during runtime using a classical compute environment that is tightly integrated with the quantum processor. For different combinations of the primitives, logical state fidelity measurements are made after applying the gate to different input states, providing bounds on the process fidelity. We find the highest fidelity operations with the color code, with the fault-tolerant SPAM operation achieving fidelities of 0.99939(15) and 0.99959(13) when preparing eigenstates of the logical X and Z operators, which is higher than the average physical qubit SPAM fidelities of 0.9968(2) and 0.9970(1) for the physical X and Z bases, respectively. When combined with a logical transversal CNOT gate, we find the color code to perform the sequence--state preparation, CNOT, measure out--with an average fidelity bounded by [0.9957,0.9963]. The logical fidelity bounds are higher than the analogous physical-level fidelity bounds, which we find to be [0.9850,0.9903], reflecting multiple physical noise sources such as SPAM errors for two qubits, several single-qubit gates, a two-qubit gate and some amount of memory error

Evaluation of surgical fixation methods for the implantation of melt electrowriting-reinforced hyaluronic acid hydrogel composites in porcine cartilage defects

The surgical repair of articular cartilage remains an ongoing challenge in orthopedics. Tissue engineering is a promising approach to treat cartilage defects; however, scaffolds must (i) possess the requisite material properties to support neocartilage formation, (ii) exhibit sufficient mechanical integrity for handling during implantation, and (iii) be reliably fixed within cartilage defects during surgery. In this study, we demonstrate the reinforcement of soft norbornene-modified hyaluronic acid (NorHA) hydrogels via the melt electrowriting (MEW) of polycaprolactone to fabricate composite scaffolds that support encapsulated porcine mesenchymal stromal cell (pMSC, three donors) chondrogenesis and cartilage formation and exhibit mechanical properties suitable for handling during implantation. Thereafter, acellular MEW-NorHA composites or MEW-NorHA composites with encapsulated pMSCs and precultured for 28 days were implanted in full-thickness cartilage defects in porcine knees using either bioresorbable pins or fibrin glue to assess surgical fixation methods. Fixation of composites with either biodegradable pins or fibrin glue ensured implant retention in most cases (80%); however, defects treated with pinned composites exhibited more subchondral bone remodeling and inferior cartilage repair, as evidenced by micro-computed tomography (micro-CT) and safranin O/fast green staining, respectively, when compared to defects treated with glued composites. Interestingly, no differences in repair tissue were observed between acellular and cellularized implants. Additional work is required to assess the full potential of these scaffolds for cartilage repair. However, these results suggest that future approaches for cartilage repair with MEW-reinforced hydrogels should be carefully evaluated with regard to their fixation approach for construct retention and surrounding cartilage tissue damage

Focal adhesion is associated with lithium response in bipolar disorder: evidence from a network-based multi-omics analysis

Lithium (Li) is one of the most effective drugs for treating bipolar disorder (BD), however, there is presently no way to predict response to guide treatment. The aim of this study is to identify functional genes and pathways that distinguish BD Li responders (LR) from BD Li non-responders (NR). An initial Pharmacogenomics of Bipolar Disorder study (PGBD) GWAS of lithium response did not provide any significant results. As a result, we then employed network-based integrative analysis of transcriptomic and genomic data. In transcriptomic study of iPSC-derived neurons, 41 significantly differentially expressed (DE) genes were identified in LR vs NR regardless of lithium exposure. In the PGBD, post-GWAS gene prioritization using the GWA-boosting (GWAB) approach identified 1119 candidate genes. Following DE-derived network propagation, there was a highly significant overlap of genes between the top 500- and top 2000-proximal gene networks and the GWAB gene list (Phypergeometric = 1.28E–09 and 4.10E–18, respectively). Functional enrichment analyses of the top 500 proximal network genes identified focal adhesion and the extracellular matrix (ECM) as the most significant functions. Our findings suggest that the difference between LR and NR was a much greater effect than that of lithium. The direct impact of dysregulation of focal adhesion on axon guidance and neuronal circuits could underpin mechanisms of response to lithium, as well as underlying BD. It also highlights the power of integrative multi-omics analysis of transcriptomic and genomic profiling to gain molecular insights into lithium response in BD.publishedVersio

A high-throughput platform for stem cell niche co-cultures and downstream gene expression analysis

Stem cells reside in 'niches', where support cells provide critical signalling for tissue renewal. Culture methods mimic niche conditions and support the growth of stem cells in vitro. However, current functional assays preclude statistically meaningful studies of clonal stem cells, stem cell-niche interactions, and genetic analysis of single cells and their organoid progeny. Here, we describe a 'microraft array' (MRA) that facilitates high-throughput clonogenic culture and computational identification of single intestinal stem cells (ISCs) and niche cells. We use MRAs to demonstrate that Paneth cells, a known ISC niche component, enhance organoid formation in a contact-dependent manner. MRAs facilitate retrieval of early enteroids for quantitative PCR to correlate functional properties, such as enteroid morphology, with differences in gene expression. MRAs have broad applicability to assaying stem cell-niche interactions and organoid development, and serve as a high-throughput culture platform to interrogate gene expression at early stages of stem cell fate choices

Quantifying the effects of bioturbation by Carcinus maenas L. (green crabs) on Zostera marina (eelgrass) transplants using mesocosm experiments

Mesocosm experiments were conducted in the summer of 1996 to quantify the effect of bioturbation by Carcinus maenas (the introduced European green crab) on survival of transplanted Zostera marina (eelgrass). The research grew out of a successful 2.52 ha eelgrass transplant project in the Great Bay Estuary of New Hampshire. At several subtidal sites, green crabs were found to damage transplanted eelgrass by cutting the shoots to the extent that some sites demonstrated poor survival. In three separate experiments, eight replicate mesocosm tanks were transplanted with 36 shoots of eelgrass, and different crab densities were introduced into the tanks. The number of shoots damaged by crabs was significantly higher in tanks with moderate (4.0 crabs/m2), high (7.0 crabs/m2), or very high (15.0 crabs/m2) crab densities than in tanks with low (1.0 crabs/m2) crab densities. Up to 39% of viable shoots were lost within one week of exposure to green crab activities. The mesocosm results demonstrated that green crabs were not directly attracted to eelgrass but that they significantly decreased transplant survival through their activity. Field densities of green crabs were found to exceed the density at which most damage occurred in the experiments, suggesting that this introduced species can be a major determinant of eelgrass transplant survival. The results underscore the major influence that biological components of transplant sites can have on transplant survival, and the need for their consideration in the site selection process

Developing success criteria for restored eelgrass, salt marsh and mud flat habitats

When estuarine habitats are restored, it is crucial to determine their success or failure. How can we tell, bringing a minimum of preconceived notions to the task and using a valid scientific process, if the functions and values of habitats have been recreated and returned to the estuary? In the New Hampshire Port Mitigation Project (1993–1995), we formulated literature-based success criteria (SC), but could not quantitatively defend their scientific validity. We are now using the project as a laboratory for developing and testing rigorous SC. We developed indicators of chosen habitat functions, then created statistical representations of natural, local reference sites for comparison to the functional development of restored habitats. An explanation of the steps in developing and testing the method are followed by a test application of our SC methodology using the data from eelgrass transplant sites (6.2 acres) created for the New Hampshire Port Mitigation Project. At the same time, we are developing a methodology for a more generic model of SC that we are applying to the restorations of salt marsh and mud flat for the Port Mitigation. We believe the methodology to develop and apply SC is transferable to other locations and habitats not only because of its objective foundation but because it is based on data collected locally