A study on the BE2100 Noninvasive Biomass Sensor as an instrument for measuring optical density during fed-batch fermentation at various stir rates

Fusion proteins, engineered proteins that combine the DNA sequences and therefore properties of two different proteins, can be used in a variety of therapeutic purposes. One example of a therapeutic fusion protein is collagen binding domain-parathyroid hormone glutathione-S-transferase (CBD-PTH-GST), which can combat osteoporosis by binding specifically to collagen in the vertebral column and promoting bone growth through the release of calcium. This fusion protein is being expressed with Escherichia coli at the University of Arkansas through fed-batch fermentation, a method that produces large volume of cells through fermentation in a controlled environment in a bioreactor. It is necessary to track cell growth during fed-batch fermentation, and typical methods include measuring optical density (OD) with a spectrophotometer. However, this machine is limited in the range of OD it can measure without dilution and requires removal of samples from the bioreactor. Alternatively a noninvasive OD probe can be used to monitor cell growth during fed-batch fermentation, such as the BE2100 Noninvasive Biomass Sensor, or BugEye probe. Unfortunately the relationship between BugEye units and spectrophotometer OD is not well understood. This study was conducted in order to investigate the relationship between the BugEye probe and spectrophotometer OD and whether or not this relationship was affected by the RPM of the stirrer in the bioreactor during fermentation

Lava field evolution and emplacement dynamics of the 2014–2015 basaltic fissure eruption at Holuhraun, Iceland

The 6-month long eruption at Holuhraun (August 2014–February 2015) in the Bárðarbunga-Veiðivötn volcanic system was the largest effusive eruption in Iceland since the 1783–1784 CE Laki eruption. The lava flow field covered ~84 km2 and has an estimated bulk (i.e., including vesicles) volume of ~1.44 km3. The eruption had an average discharge rate of ~90 m3/s making it the longest effusive eruption in modern times to sustain such high average flux. The first phase of the eruption (August 31, 2014 to mid-October 2014) had a discharge rate of ~350 to 100 m3/s and was typified by lava transport via open channels and the formation of four lava flows, no. 1–4,which were emplaced side by side. The eruption began on a 1.8 km long fissure, feeding partly incandescent sheets of slabby pāhoehoe up to 500 m wide. By the following day the lava transport got confined to open channels and the dominant lava morphology changed to rubbly pāhoehoe and ‘a’ā. The latter became the dominating morphology of lava flows no. 1–8. The second phase of the eruption (Mid-October to end November) had a discharge of ~100–50 m3/s. During this time the lava transport system changed, via the formation of a b1 km2 lava pond ~1 km east of the vent. The pond most likely formed in a topographical low created by a the pre-existing Holuhraun and the newHoluhraun lava flow fields. This pond became themain point of lava distribution, controlling the emplacement of subsequent flows (i.e. no. 5–8). Towards the end of this phase inflation plateaus developed in lava flowno. 1. These inflation plateaus were the surface manifestation of a growing lava tube system, which formed as lava ponded in the open lava channels creating sufficient lavastatic pressure in the fluid lava to lift the roof of the lava channels. This allowed new lava into the previously active lava channel lifting the channel roof via inflation. The final (third) phase, lasting from December to end-February 2015 had a mean discharge rate of ~50 m3/s. In this phase the lava transport was mainly confined to lava tubes within lava flows no. 1–2, which fed breakouts that resurfaced N19 km2 of the flow field. The primary lava morphology from this phase was spiny pāhoehoe, which superimposed on the ‘a’ā lava flows no. 1–3 and extended the entire length of the flow field (i.e. 17 km). Thismade the 2014–2015 Holuhraun a paired flow field,where both lava morphologies had similar length. We suggest that the similar length is a consequence of the pāhoehoe is fed from the tube systemutilizing the existing ‘a’ā lava channels, and thereby are controlled by the initial length of the ‘a’ā flows.The work was financed with crisis response funding from the Icelandic Government along with European Community's Seventh Framework Programme Grant No. 308377 (Project FUTUREVOLC) and along with the Icelandic Research fund, Rannis, Grant of Excellence No. 152266-052 (Project EMMIRS). Furthermore, Vinur Vatnajökuls are thanked for support.Peer Reviewe

Atlas of group A streptococcal vaccine candidates compiled using large-scale comparative genomics.

Group A Streptococcus (GAS; Streptococcus pyogenes) is a bacterial pathogen for which a commercial vaccine for humans is not available. Employing the advantages of high-throughput DNA sequencing technology to vaccine design, we have analyzed 2,083 globally sampled GAS genomes. The global GAS population structure reveals extensive genomic heterogeneity driven by homologous recombination and overlaid with high levels of accessory gene plasticity. We identified the existence of more than 290 clinically associated genomic phylogroups across 22 countries, highlighting challenges in designing vaccines of global utility. To determine vaccine candidate coverage, we investigated all of the previously described GAS candidate antigens for gene carriage and gene sequence heterogeneity. Only 15 of 28 vaccine antigen candidates were found to have both low naturally occurring sequence variation and high (>99%) coverage across this diverse GAS population. This technological platform for vaccine coverage determination is equally applicable to prospective GAS vaccine antigens identified in future studies

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

Proceedings of the 3rd Biennial Conference of the Society for Implementation Research Collaboration (SIRC) 2015: advancing efficient methodologies through community partnerships and team science

It is well documented that the majority of adults, children and families in need of evidence-based behavioral health interventionsi do not receive them [1, 2] and that few robust empirically supported methods for implementing evidence-based practices (EBPs) exist. The Society for Implementation Research Collaboration (SIRC) represents a burgeoning effort to advance the innovation and rigor of implementation research and is uniquely focused on bringing together researchers and stakeholders committed to evaluating the implementation of complex evidence-based behavioral health interventions. Through its diverse activities and membership, SIRC aims to foster the promise of implementation research to better serve the behavioral health needs of the population by identifying rigorous, relevant, and efficient strategies that successfully transfer scientific evidence to clinical knowledge for use in real world settings [3]. SIRC began as a National Institute of Mental Health (NIMH)-funded conference series in 2010 (previously titled the “Seattle Implementation Research Conference”; $150,000 USD for 3 conferences in 2011, 2013, and 2015) with the recognition that there were multiple researchers and stakeholdersi working in parallel on innovative implementation science projects in behavioral health, but that formal channels for communicating and collaborating with one another were relatively unavailable. There was a significant need for a forum within which implementation researchers and stakeholders could learn from one another, refine approaches to science and practice, and develop an implementation research agenda using common measures, methods, and research principles to improve both the frequency and quality with which behavioral health treatment implementation is evaluated. SIRC’s membership growth is a testament to this identified need with more than 1000 members from 2011 to the present.ii SIRC’s primary objectives are to: (1) foster communication and collaboration across diverse groups, including implementation researchers, intermediariesi, as well as community stakeholders (SIRC uses the term “EBP champions” for these groups) – and to do so across multiple career levels (e.g., students, early career faculty, established investigators); and (2) enhance and disseminate rigorous measures and methodologies for implementing EBPs and evaluating EBP implementation efforts. These objectives are well aligned with Glasgow and colleagues’ [4] five core tenets deemed critical for advancing implementation science: collaboration, efficiency and speed, rigor and relevance, improved capacity, and cumulative knowledge. SIRC advances these objectives and tenets through in-person conferences, which bring together multidisciplinary implementation researchers and those implementing evidence-based behavioral health interventions in the community to share their work and create professional connections and collaborations

The Endourological Society Inaugural Census Report

The Endourological Society, the premier urological society encompassing endourology, robotics and focal surgery, is composed of a diverse group of over 1,300 urologists. However, limited information has been collected about society members. Recognizing this need, a survey was initiated to capture data regarding current member practices, as well as help the society shape the future direction of the organization. Presented herein is the inaugural Endourological Society census report as the beginning of a continued effort for global improvement in the field of endourology. Using a REDCap® database, an email survey was circulated to the membership of the Endourological Society from May through June 2021. Twenty questions were posed, categorizing member data in terms of epidemiology/demographics, practice patterns, member opinions, and future educational preferences. Responses were received from 534 members, representing 40.3% of membership. Data demonstrated that the average age, sex, race, and ethnicity of the typical Society member respondent is a 48-year-old Caucasian male working in the United States, with a mean of 25 years in practice. Retrograde endoscopy and percutaneous nephrolithotomy were identified as the most common practice skills, and 50% of members are involved in robotics. Importantly, the census confirmed that the World Congress of Endourology and Technology (WCET) remains popular with Society members as a means of educational advancement. To sustain and advance the Society, information is required to understand the career interests and future educational desires of its members. This inaugural census provides crucial data regarding its membership and how the Society can achieve continued success and adjust its focus. Future census efforts will expand on the initial findings and stratify the data to elucidate changes in the needs of the Society as a whole. Circulating an annual census will allow for continued improvements in the field of endourology, and ultimately, better care for urologic patients

String Area Recital

1.5Full digital generat a partir de la base topogràfica 1:5 000. Els fulls d'aquesta sèrie corresponen a la divisió 4 x 4 de la malla de distribució del Mapa topográfico nacional de España 1:50 000. Cada full inclou 2 finestres (Mapa índex de la sèrie; Mapa guia). - Projecció Universal Transversa Mercator (UTM), fus 31, sobre el·lipsoide internacional i datum europeu. Equidistància de les corbes de nivell: 5 m.Imatge digital de 90 x 67 cm1:5 000300 PP

A chromosome-scale epigenetic map of the Hydra genome reveals conserved regulators of cell state.

The epithelial and interstitial stem cells of the freshwater polyp Hydra are the best-characterized stem cell systems in any cnidarian, providing valuable insight into cell type evolution and the origin of stemness in animals. However, little is known about the transcriptional regulatory mechanisms that determine how these stem cells are maintained and how they give rise to their diverse differentiated progeny. To address such questions, a thorough understanding of transcriptional regulation in Hydra is needed. To this end, we generated extensive new resources for characterizing transcriptional regulation in Hydra, including new genome assemblies for Hydra oligactis and the AEP strain of Hydra vulgaris, an updated whole-animal single-cell RNA-seq atlas, and genome-wide maps of chromatin interactions, chromatin accessibility, sequence conservation, and histone modifications. These data revealed the existence of large kilobase-scale chromatin interaction domains in the Hydra genome that contain transcriptionally coregulated genes. We also uncovered the transcriptomic profiles of two previously molecularly uncharacterized cell types: isorhiza-type nematocytes and somatic gonad ectoderm. Finally, we identified novel candidate regulators of cell type-specific transcription, several of which have likely been conserved at least since the divergence of Hydra and the jellyfish Clytia hemisphaerica more than 400 million years ago

Serological Evidence of Immune Priming by Group A Streptococci in Patients with Acute Rheumatic Fever

Acute rheumatic fever (ARF) is an autoimmune response to Group A Streptococcus (GAS) infection. Repeated GAS exposures are proposed to ‘prime’ the immune system for autoimmunity. This notion of immune-priming by multiple GAS infections was first postulated in the 1960s, but direct experimental evidence to support the hypothesis has been lacking. Here we present novel methodology, based on antibody responses to GAS T‑antigens, that enables previous GAS exposures to be mapped in patient sera. T-antigens are surface expressed, type specific antigens and GAS strains fall into 18 major clades or T-types. A panel of recombinant T-antigens was generated and immunoassays were performed in parallel with serum depletion experiments allowing type-specific T‑antigen antibodies to be distinguished from cross-reactive antibodies. At least two distinct GAS exposures were detected in each of the ARF sera tested. Furthermore, no two sera had the same T-antigen reactivity profile suggesting that each patient was exposed to a unique series of GAS T‑types prior to developing ARF. The methods have provided much-needed experimental evidence to substantiate the immune-priming hypothesis, and will facilitate further serological profiling studies that explore the multifaceted interactions between GAS and the host