bluuebunny/crossref_metadata_2025_split huggingface dataset:
High density cultivation for efficient sesquiterpenoid biosynthesis inSynechocystissp. PCC 6803
Authors: Dienst Dennis , Wichmann Julian , Mantovani Oliver , Rodrigues João , Lindberg Pia 
Published: November 2019

AbstractCyanobacteria and microalgae are attractive phototrophic host systems for climate-friendly production of fuels and other high-value chemicals. The biosynthesis of an increasing diversity of industrially relevant compounds such as terpenoids has been demonstrated in recent years. To develop economically feasible and sustainable process designs, major challenges still remain regarding intracellular carbon partitioning, specific metabolic pathway activities and efficient cultivation strategies. Here, we present a technical study on comparative characteristics of sesquiterpene and sesquiterpene alcohol accumulation in engineered strains ofSynechocystissp. PCC 6803 (substrain GT-U) under different growth conditions and cell densities. This study particularly focuses on the basic applicability of a commercial High Density Cultivation platform in the presence of a dodecane overlay, which serves as a standardin-situextractant and sink for various hydrophobic biochemicals. Significantly, the presented data demonstrate high volumetric productivities of (E)-α-bisabolene under high-density conditions that are more than two orders of magnitude higher than previously reported for cyanobacteria. Operating in a two-step semi-batch mode over a period of eight days, average final volumetric titers of 179.4 ± 20.7 mg * L−1were detected. Likewise, the sesquiterpene alcohols (-)-patchoulol and (-)-α-bisabolol accumulated to many times higher levels in high density cultivation than under standard batch conditions, with final titers of 17.3 ± 1.85 mg * L−1and 96.3 ± 2.2 mg * L−1, respectively. In contrast, specific product accumulation (mg * L−1* OD750−1) was compromised particularly for bisabolene in the high density system during phases of high biomass accumulation rates. Volumetric productivities were high during linear growth at high densities, distinctly outperforming standard batch systems. While the presented data highlight the benefits of high-density strategies for highly efficient phototrophic terpenoid production, they further point at the presence of major metabolic bottlenecks for engineered terpenoid biosynthesis and the requirement for systematic and/or targeted strategies to sustainably redirect inherent carbon fluxes in cyanobacteria. Together, our data provide additional insights into growth- and density-related effects on the efficiency of product accumulation, introducing low-scale High Density Cultivation as a rapid and efficient platform for screening of heterologous terpenoid production in cyanobacteria.
Metric learning enables synthesis of heterogeneous single-cell modalities
Authors: Singh Rohit , Hie Brian , Narayan Ashwin , Berger Bonnie 
Published: November 2019

AbstractA complete understanding of biological processes requires synthesizing information across heterogeneous modalities, such as age, disease status, or gene/protein expression. Until recently, single-cell profiling experiments could measure only a single modality, leading to analysis focused on integrating information across separate experiments. However, researchers can now measure multiple modalities simultaneously in a single experiment, providing a new data paradigm that enables biological discovery but also requires new conceptual and analytic models. We therefore present Schema, an algorithm that leverages a principled metric learning strategy to synthesize multimodal information from the same experiment. To demonstrate the flexibility and power of our approach, we use Schema to infer cell types by integrating gene expression and chromatin accessibility data, perform differential gene expression analysis while accounting for batch effects and developmental age, estimate evolutionary pressure on peptide sequences, and synthesize spliced and unspliced mRNA data to infer cell differentiation. Schema can synthesize arbitrarily many modalities and capture sophisticated relationships between them, is computationally efficient, and provides a valuable conceptual model for exploring and understanding complex biology.
Blinking Statistics and Molecular Counting in direct Stochastic Reconstruction Microscopy (dSTORM)
Authors: Patel Lekha , Williamson David , Owen Dylan M. , Cohen Edward A.K. 
Published: November 2019

AbstractMotivationMany recent advancements in single molecule localisation microscopy exploit the stochastic photo-switching of fluorophores to reveal complex cellular structures beyond the classical diffraction limit. However, this same stochasticity makes counting the number of molecules to high precision extremely challenging, preventing key insight into the cellular structures and processes under observation.ResultsModelling the photo-switching behaviour of a fluorophore as an unobserved continuous time Markov process transitioning between a single fluorescent and multiple dark states, and fully mitigating for missed blinks and false positives, we present a method for computing the exact probability distribution for the number of observed localisations from a single photo-switching fluorophore. This is then extended to provide the probability distribution for the number of localisations in a dSTORM experiment involving an arbitrary number of molecules. We demonstrate that when training data is available to estimate photo-switching rates, the unknown number of molecules can be accurately recovered from the posterior mode of the number of molecules given the number of localisations. Finally, we demonstrate the method on experimental data by quantifying the number of adapter protein Linker for Activation of T cells (LAT) on the cell surface of the T cell immunological synapse.AvailabilitySoftware available at https://github.com/lp1611/mol_count_dstorm.
Dynamic Bayesian networks for integrating multi-omics time-series microbiome data
Authors: Ruiz-Perez Daniel , Lugo-Martinez Jose , Bourguignon Natalia , Mathee Kalai , Lerner Betiana , Bar-Joseph Ziv , Narasimhan Giri 
Published: November 2019

ABSTRACTA key challenge in the analysis of longitudinal microbiome data is the inference of temporal interactions between microbial taxa, their genes, the metabolites they consume and produce, and host genes. To address these challenges we developed a computational pipeline, PALM, that first aligns multi-omics data and then uses dynamic Bayesian networks (DBNs) to reconstruct a unified model. Our approach overcomes differences in sampling and progression rates, utilizes a biologically-inspired multi-omic framework, reduces the large number of entities and parameters in the DBNs, and validates the learned network. Applying PALM to data collected from inflammatory bowel disease patients, we show that it accurately identifies known and novel interactions. Targeted experimental validations further support a number of the predicted novel metabolite-taxa interactions.Source code and data will be freely available after publication under the MIT Open Source license agreement on our GitHub page.IMPORTANCEWhile a number of large consortia are collecting and profiling several different types of microbiome and genomic time series data, very few methods exist for joint modeling of multi-omics data sets. We developed a new computational pipeline, PALM, which uses Dynamic Bayesian Networks (DBNs) and is designed to integrate multi-omics data from longitudinal microbiome studies. When used to integrate sequence, expression, and metabolomics data from microbiome samples along with host expression data, the resulting models identify interactions between taxa, their genes and the metabolites they produce and consume, and their impact on host expression. We tested the models both by using them to predict future changes in microbiome levels, and by comparing the learned interactions to known interactions in the literature. Finally, we performed experimental validations for a few of the predicted interactions to demonstrate the ability of the method to identify novel relationships and their impact.
Lis1 regulates Phagocytosis by co-localising with actin in the Phagocytic cup
Authors: Chhatre Aditya , Sanghavi Paulomi , Mallik Roop 
Published: November 2019

AbstractPhagocytosis, the ingestion of solid particles by cells, is essential for nutrient uptake, innate immune response, antigen presentation and organelle homeostasis. Here we show that Lissencephaly-1 (Lis1), a well-known regulator of the microtubule motor Dynein, also co-localises with actin at the phagocytic cup in the early stages of phagocytosis. Both knockdown and overexpression of Lis1 perturbs phagocytosis, suggesting that an optimum level of Lis1 is required to regulate actin dynamics within the phagocytic cup during particle engulfment. This requirement of Lis1 is replicated in mouse macrophage cells as well as in the amoebaDictyostelium, indicating an evolutionarily conserved role for Lis1 in phagocytosis. In support of these findings, a general role for Lis1 in regulating actin dynamics is suggested by observing defective migration of cells overexpressing Lis1. Taken together, Lis1 localises to the phagocytic cup and influences actin dynamics in a manner that is important for the uptake of solid particles in cells.
Biophysical models of cis-regulation as interpretable neural networks
Authors: Tareen Ammar , Kinney Justin B. 
Published: November 2019

AbstractThe adoption of deep learning techniques in genomics has been hindered by the difficulty of mechanistically interpreting the models that these techniques produce. In recent years, a variety of post-hoc attribution methods have been proposed for addressing this neural network interpretability problem in the context of gene regulation. Here we describe a complementary way of approaching this problem. Our strategy is based on the observation that two large classes of biophysical models of cis-regulatory mechanisms can be expressed as deep neural networks in which nodes and weights have explicit physiochemical interpretations. We also demonstrate how such biophysical networks can be rapidly inferred, using modern deep learning frameworks, from the data produced by certain types of massively parallel reporter assays (MPRAs). These results suggest a scalable strategy for using MPRAs to systematically characterize the biophysical basis of gene regulation in a wide range of biological contexts. They also highlight gene regulation as a promising venue for the development of scientifically interpretable approaches to deep learning.
The pattern of interaction political actors on situations of tenurial conflict in watershed
Authors: Anwar Khairul 
Published: November 2019

PurposeThis paper aims to find the pattern of interaction of political actors in situations of tenurial conflict in the watershed through a review of cases of social conflicts of plantation villages around Siak watershed 2009-2014.Design/methodology/approachIn harmony with the Research Master Plan (RIP) of Riau University, the socio-political of Riau Malay society and the fundamental scientific pattern of Riau university, the development of the resources of area and waters and Malay culture, since 2001, the writer has conducted a study related to the issues of natural resources policy, especially oil palm in the era of regional autonomy and decentralization. This is in line with the umbrella of research developed by the University of Riau namely studying various aspects of natural resources (especially oil palm) and human resources of Watershed (DAS). The writer's review is; first, the dynamics of politics in relation to the issue of oil palm plantation policy in Riau. This study shows that there are many central policies when implemented at the local level including watersheds clashing with local interests such as forests and land ownership. Second, the writer has also reviewed the policy issues and problems of oil palm plantations in Riau watershed in 2000. This study shows there are many issues and problems formulated differently by different people.FindingsMapping and strategy are examined through the study of political strategies on oil palm plantations and use them to answer the following two questions: what kind of political model which can be used to manage the watershed conflict since regional autonomy is implemented. Economic factors are influential in mapping and management strategies for the emergence of tenurial conflicts in the Siak River Rivershed 2009-2014. The tenurial conflict management model of Siak rivershed, which is considered relevant, is a conflict-based model of cooperation with a partnership pattern between local government, watershed civil society and plantation business actors. The change of agrarian structure is directed to the effort to open the space for the accesibility of society in decision-making.Originality/valueSome of these studies have not reached the tenurial conflicts in the watershed areas, especially Siak watershed. In fact, about 80 per cent of Riau province region consists of watershed. This becomes the originality and gap of this study with previous studies. This research was conducted further as an effort to synergize Riau's development policy with Riau University's research in harmony with RIP that was created and aimed to find the pattern of interaction of political actors in situations of tenurial conflict in Watershed through a review of cases of social conflicts of plantation around Siak watershed in 2009-2014.
Phylogenetic and structural diversity of aromatically dense pili from environmental metagenomes
Authors: Bray Marcus S. , Wu Jieying , Padilla Cory C. , Stewart Frank J. , Fowle David A. , Henny Cynthia , Simister Rachel L. , Thompson Katharine J. , Crowe Sean A. , Glass Jennifer B. 
Published: November 2019

SummaryElectroactive type IV pili, or e‐pili, are used by some microbial species for extracellular electron transfer. Recent studies suggest that e‐pili may be more phylogenetically and structurally diverse than previously assumed. Here, we used updated aromatic density thresholds (≥9.8% aromatic amino acids, ≤22‐aa aromatic gaps and aromatic amino acids at residues 1, 24, 27, 50 and/or 51, and 32 and/or 57) to search for putative e‐pilin genes in metagenomes from diverse ecosystems with active microbial metal cycling. Environmental putative e‐pilins were diverse in length and phylogeny, and included truncated e‐pilins in Geobacter spp., as well as longer putative e‐pilins in Fe(II)‐oxidizing Betaproteobacteria and Zetaproteobacteria.
Development of a peri‐implantitis model in the rat
Authors: Sun Jingqing , Eberhard Joerg , Glage Silke , Held Nadine , Voigt Henning , Schwabe Kerstin , Winkel Andreas , Stiesch Meike 
Published: November 2019

AbstractObjectivesThe aim of the present study was to establish a rodent peri‐implantitis model induced by a mixed bacterial infection characterized by bone loss and semi‐quantitative graduation of peri‐implant inflammation in histological sections.Materials and MethodsTwo titanium implants were implanted in Sprague‐Dawley rats, bilaterally in each maxilla. After 3 weeks healing, the rats were randomized into three groups according to different treatments over the next 3 months: Antibiotic‐Group with oral lavage of antibiotics; Bacteria‐Group with oral lavage of Streptococcus oralis and Aggregatibacter actinomycetemcomitans; and Untreated Group with standard housing and no additional treatment. Maxillae were dissected to perform microscopic and histological analysis of bone height and peri‐implant tissues.ResultsThe bone level, measured at one implant site per animal, in the Bacteria‐Group (2.60 ± 0.39 mm) was significantly reduced compared to the Antibiotic‐Group (2.29 ± 0.32 mm) after 3 months. The differences of bone height in the Bacteria‐Group and the Untreated Group (2.46 ± 0.27 mm) did not reach statistical significance. The inflammatory response with respect to the number of inflammatory cells and fibrous tissue compartments of the peri‐implant tissues in the Bacteria‐Group was significantly increased compared with the Antibiotic‐Group (p < .05). S. oralis and A. actinomycetemcomitans DNAs were detected in the Bacteria‐Group.ConclusionsThis rat model of peri‐implantitis used oral bacterial lavage for the induction of an inflammatory host response and bone loss. Additional bacterial treatment enhances the peri‐implant phenotype, so that significant differences to a reduced bacterial load similar to the human peri‐implantitis disease can be identified.
Daily activity performance in congenital and childhood forms of myotonic dystrophy type 1: a population‐based study
Authors: Eriksson Britt‐Marie , Ekström Anne‐Berit , Peny‐Dahlstrand Marie 
Published: November 2019

AimsTo identify and describe the profile characterizing motor and process skills during daily activity performance in individuals with congenital and childhood forms of myotonic dystrophy type 1 (DM1) and to investigate differences in performance between subgroups.MethodSixty participants (34 males, 26 females, mean age=17y 8mo, SD=6y 0mo, range 5y 8mo–29y 0mo) were divided into severe congenital (n=9), mild congenital (n=20), and childhood (n=31) DM1 subgroups. Daily activity performance was evaluated using a standardized observational instrument: the Assessment of Motor and Process Skills.ResultsDeficits in performance were more pronounced in process than motor skills. Performance more than 2 SDs below age‐specific norms was seen in 65% of participants for process skills and 33% of participants for motor skills. The cut‐off scores indicated a potential need for assistance in daily activities for 79% of participants older than 18 years of age (n=28) due to deficient process skills.InterpretationExtensive deficits in daily activity performance were found in congenital and childhood forms of DM1, mainly owing to deficient process skills. Such skills impact on the ability to perform daily activities and could explain dependency in individuals with DM1. Process skills should be considered when evaluating daily activity performance.What this paper adds

Young people with myotonic dystrophy type 1 show deficits in motor and process skills when performing daily activities, compared with normative data.

Deficits in process skills were more pronounced than deficits in motor skills.
Intramural jejunal leiomyoma as a cause of colic
Authors: Miles S. , Davis W. , Craft W. F. 
Published: November 2019

SummaryA 15‐year‐old Thoroughbred gelding showjumper presented with colic after a history of chronic mild, intermittent colic. He was refractory to medical management. At surgery, he was found to have a 15‐cm intramural mass in the distal jejunum, approximately 3 m orad to the ileum. Histopathology post‐operatively revealed a leiomyoma. Leiomyomas in horses are rare. They have been reported most commonly in the reproductive tract, with other rare reports in the oesophagus and omentum. To the knowledge of the authors, there are no reports of identification and treatment of non‐strangulating obstruction of the jejunum caused by a leiomyoma. The horse recovered from his surgery and went on to compete at the same level of showjumping as previous to the surgery with no further episodes of colic. Based on this report, leiomyoma should be a differential for small intestinal obstruction in the future.
Animal transgenesis now and beyond in the era of genome editing: Snapshots from the 15th Transgenic Technology Meeting (TT2019) in Kobe, Japan
Authors: Kiyonari Hiroshi , Furuta Yasuhide 
Published: November 2019

AbstractThe 15th Transgenic Technology (TT) Meeting of the International Society for Transgenic Technologies (ISTT) was held for the first time in Japan in April of 2019 (TT2019). Delegates from around the world, including researchers, technicians and trainees, spent an exciting 4 days, engaging in scientific and technical discussions, information sharing and networking. In the era of genome editing, CRISPR technologies prevailed as popular subjects of discussion throughout the meeting on topics ranging from their applications in the mouse and growing number of other research and industrial animal species, technical challenges in the production of genome‐edited animals, to ethical considerations in biomedical research. In particular, impressive progress was reported on the use of CRISPR technologies in nonconventional animal models and large mammalian species in biomedical and industrial settings, indicating areas of expanding frontiers in animal transgenesis. Amid growing excitement with genome editing technologies, reports on conventional genetic engineering approaches and reproductive biology techniques demonstrated that these techniques remain essential to meet the demanding needs of generating complex genome modifications, complementing genome editing approaches. TT2019 was a great success, concluding with a widely shared appreciation of the current field and hints for future directions of animal transgenesis.
Missiological Framework in Africa
Authors: Isaak Paul John 
Published: November 2019

AbstractThis article has three parts. First, it deals with the understanding of mission in the context of Namibia. Second, it offers a profile of African spirituality and its politico‐socio‐economic implications, or with the missionary orthopraxis, in light of the African parable of the awakening giant. And third, it focuses on the African missional church and its missionary praxis. The paper argues that the triune God creates the church and sustains it through the gifts of word and sacrament by the power of the Spirit. Such a missional church understands its participation in God's mission (missio Dei) as contextual by addressing faithfully the challenges in a comprehensive and holistic way.
The Apostolic Faith Mission
Authors: Chikane Frank 
Published: November 2019

AbstractThe Apostolic Faith Mission (AFM) is a classical Pentecostal church born in May 1908, influenced by the April 1906 Azusa Street Revival in Los Angeles. It was also born two years before the Edinburgh World Missionary Conference. Between then and now, the AFM followed a lone mission and evangelism journey outside the World Missionary conferences and the conferences on World Mission and Evangelism. Although the AFM grew from South Africa to six continents, its growth was encumbered by racist and colonial perspectives of mission and evangelism. Its first wave of missions was led by Indigenous South Africans at the Revival in Doornfontein and those from the neighbouring countries who worked in mines in South Africa. The second wave included organized missions by white South Africans, who unfortunately had to pull back from Southern African countries because of intensified struggles for liberation. The third wave was by local congregations that formed hubs for missions to specific countries (India and Pakistan). The fourth wave was by Zimbabweans who left their country because of difficult economic conditions. The isolation of the black churches in South Africa based on the influence of apartheid policies allowed black members to develop their own local ecumenical perspectives, which enabled them to have a broader understanding of mission and evangelism. This helped the church to move into the ecumenical world following the unity of the church.