bluuebunny/crossref_metadata_2025_split huggingface dataset:
Emergence of stable coexistence in a complex microbial community through metabolic cooperation and spatio-temporal niche partitioning
Authors: Blasche Sonja , Kim Yongkyu , Mars Ruben , Kafkia Eleni , Maansson Maria , Machado Daniel , Teusink Bas , Nielsen Jens , Benes Vladimir , Neves Rute , Sauer Uwe , Patil Kiran Raosaheb 
Published: February 2019

SummaryMicrobial communities in nature often feature complex compositional dynamics yet also stable coexistence of diverse species. The mechanistic underpinnings of such dynamic stability remain unclear as system-wide studies have been limited to small engineered communities or synthetic assemblies. Here we show how kefir, a natural milk-fermenting community, realizes stable coexistence through spatio-temporal orchestration of species and metabolite dynamics. During milk fermentation, kefir grains (a polysaccharide matrix synthesized by kefir microbes) grow in mass but remain unchanged in composition. In contrast, the milk is colonized in a dynamic fashion with early members opening metabolic niches for the followers. Through large-scale mapping of metabolic preferences and inter-species interactions, we show how microbes poorly suited for milk survive in, and even dominate, the community through metabolic cooperation and uneven partitioning between the grain and the liquid phase. Overall, our findings reveal how spatio-temporal dynamics promote stable coexistence and have implications for deciphering and modulating complex microbial ecosystems.
From expression footprints to causal pathways: contextualizing large signaling networks with CARNIVAL
Authors: Liu Anika , Trairatphisan Panuwat , Gjerga Enio , Didangelos Athanasios , Barratt Jonathan , Saez-Rodriguez Julio 
Published: February 2019

AbstractWhile gene expression profiling is commonly used to gain an overview of cellular processes, the identification of upstream processes that drive expression changes remains a challenge. To address this issue, we introduce CARNIVAL, a causal network building tool which derives network architectures from gene expression footprints.CARNIVAL (CAusal Reasoning pipeline for Network identification using Integer VALue programming) integrates different sources of prior knowledge, including signed and directed protein-protein interactions, transcription factor targets, and pathway signatures. The use of prior knowledge in CARNIVAL allows the capture of a broad set of upstream cellular processes and regulators, which in turn delivered results with higher accuracy when benchmarked against related tools. Implementation as an integer linear programming (ILP) problem also guarantees efficient computation. As a case study, we applied CARNIVAL to contextualize signaling networks from gene expression data in IgA nephropathy, a chronic kidney disease. CARNIVAL identified specific signaling pathways and associated mediators with important bioactivity in IgAN including WNT and TGF-β, that we subsequently validated experimentally.In summary, we demonstrated how CARNIVAL generates hypotheses on potential upstream alterations that propagate through signaling networks, providing valuable insights into disease processes. CARNIVAL, freely available as an R-package at https://saezlab.github.io/CARNIVAL, can be applied to any field of biomedical research to contextualize signaling networks and identify the causal relationships between downstream gene expression and upstream regulators.
Accurate and Efficient KIR Gene and Haplotype Inference from Genome Sequencing Reads with Novel K-mer Signatures
Authors: Roe David , Kuang Rui 
Published: February 2019

AbstractThe killer cell immunoglobulin-like receptor (KIR) proteins evolve to fight viruses and mediate the body’s reaction to pregnancy. These roles provide selection pressure for variation at both the structural/haplotype and base/allele levels. At the same time, the genes have evolved relatively recently by tandem duplication and therefore exhibit very high sequence similarity over thousands of bases. These variation-homology patterns make it impossible to interpret KIR haplotypes from abundant short-read genome sequencing data at population scale using existing methods. Here, we developed an efficient computational approach for in silico KIR probe interpretation (KPI) to accurately interpret individual’s KIR genes and haplotype-pairs from KIR sequencing reads. We designed synthetic 25-base sequence probes by analyzing previously reported haplotype sequences, and we developed a bioinformatics pipeline to interpret the probes in the context of 16 KIR genes and 16 haplotype structures. We demonstrated its accuracy on a synthetic data set as well as a real whole genome sequences from 748 individuals from The Genome of the Netherlands (GoNL). The GoNL predictions were compared with predictions from SNP-based predictions. Our results show 100% accuracy rate for the synthetic tests and a 99.6% family-consistency rate in the GoNL tests. Agreement with the SNP-based calls on KIR genes ranges from 72-100% with a mean of 92%; most differences occur in genes KIR2DS2, KIR2DL2, KIR2DS3, and KIR2DL5 where KPI predicts presence and the SNP-based interpretation predicts absence. Overall, the evidence suggests that KPI’s accuracy is 97% or greater for both KIR gene and haplotype-pair predictions, although the presence/absence genotyping leads to ambiguous haplotype-pair predictions with 16 reference KIR haplotype structures. KPI is free, open, and easily executable as a Nextflow workflow supported by a Docker environment at https://github.com/droeatumn/kpi.
The dynamics of the HIV-1 latent reservoir – considering the heterogeneous subpopulations
Authors: Ke Ruian , Deng Kai 
Published: February 2019

AbstractA major barrier to finding a cure for human immunodeficiency virus type-I (HIV-1) infection is the existence and persistence of the HIV-1 latent reservoir. Although the size of the reservoir is shown to be extremely stable under effective antiretroviral therapy, multiple lines of evidence suggest that the reservoir is composed of dynamic and heterogeneous subpopulations. Quantifying the dynamics of these subpopulations and the processes that maintain the latent reservoir is crucial to the development of effective strategies to eliminate this reservoir. Here, we constructed a mathematical model to consider four latently infected subpopulations, according to their ability to proliferate and the type of virus they are infected. Our model explains a wide range of clinical observations, including variable estimates of the reservoir half-life and dynamical turnover of cytotoxic T lymphocyte (CTL) escape viruses in the reservoir. It suggests that very early treatment leads to a reservoir that is small in size and is composed of less stable latently infected cells (compared to the reservoir in chronically infected individuals). The shorter half-lives estimated from individuals treated during acute infection is likely driven by cells that are less prone to proliferate; in contrast, the remarkably consistent estimate of the long half-lives in individuals who are treated during chronic infection are driven by fast proliferating cells that are likely to be infected by CTL escape mutants. Our model shed light on the dynamics of the reservoir in the absence and presence of antiretroviral therapy. More broadly, it can be used to estimate the turnover rates of subpopulations of the reservoir as well as to design and evaluate the impact of various therapeutic interventions to purge the HIV-1 reservoir.Author summaryHuman immunodeficiency virus (HIV) infects tens of millions of people globally and causes approximately a million death each year. Current treatment for HIV infection suppresses viral load but does not eradicates the virus. A major barrier to cure HIV infection is the existence and persistence of populations of cells that are latently infected by HIV, i.e. the HIV latent reservoir. Understanding and quantifying the kinetics of the reservoir is therefore critical for developing and evaluating effective therapies to purge the reservoir. Recent studies suggested that this reservoir is heterogenous in their population dynamics; yet most previous mathematical models consider this reservoir as a homogenous population. Here we developed a model explicitly tracking the heterogenous subpopulations of the reservoir. We show that this model explains a wide range of clinical observations, and then demonstrate its utility to make quantitative predictions about varies interventions that aim to restrict or reduce the size of the reservoir.
The structure of a highly conserved picocyanobacterial protein reveals a Tudor domain with a novel tRNA binding function
Authors: Bauer Katherine M , Dicovitsky Rose , Pellegrini Maria , Zhaxybayeva Olga , Ragusa Michael J 
Published: February 2019

ABSTRACTCyanobacteria of the Prochlorococcus and marine Synechococcus genera are the most abundant photosynthetic microbes in the ocean. Intriguingly, the genomes of these bacteria are very divergent even within each genus, both in gene content and at amino acid level of the encoded proteins. One striking exception to this is a 62 amino acid protein, termed Prochlorococcus/SynechococcusHyper Conserved Protein (PSHCP). PSHCP is not only found in all sequenced Prochlorococcus and marine Synechococcus genomes but it is also nearly 100% identical in its amino acid sequence across all sampled genomes. Such universal distribution and sequence conservation suggests an essential cellular role of the encoded protein in these bacteria. However, the function of PSHCP is unknown. We used Nuclear Magnetic Resonance (NMR) spectroscopy to determine its structure. We found that 52 of the 62 amino acids in PSHCP form a Tudor domain, while the remainder of the protein is disordered. NMR titration experiments revealed that PSHCP has only a weak affinity for DNA, but an 18.5 fold higher affinity for tRNA, hinting at an involvement of PSHCP in translation. Computational docking and mutagenesis studies identified a positively charged patch surrounding residue K30 that serves as the primary docking site for tRNA on PSHCP. These results provide the first insight into the structure and function of PSHCP and suggest a new function for Tudor domains in recognizing tRNA.
Neutral processes and high inter-annual turnover shape the assembly of soil bacterial communities in a Mediterranean watershed
Authors: Tsiknia Myrto , Fodelianakis Stilianos , Nikolaidis Nikolaos P. , Paranychianakis Nikolaos V. 
Published: February 2019

AbstractThere is a renewed interest in recent years on the ecological processes (stochastic vs selective) driving the assembly of microbial communities. Such information could potentially improve our understanding on ecosystem functioning and resilience to disturbances, ecosystem response to environmental shifts, and adoption of sustainable soil management practices. Herein, employing a suite of existing methodologies, we show that stochastic processes have an important role on the assembly of soil bacterial communities at a Mediterranean watershed. Moreover, we document that the relative contribution of assembly processes varies over the years. The observed intensification of stochastic processes was accompanied by a decrease in the contribution of variable selection in favor of homogeneous selection and dispersal and this trend was only marginally affected by land use (natural vs agricultural lands) or soil depth. Our study also revealed a high inter-annual turnover of soil microbial communities that was likely stimulated by the weak environmental selection and the prevailing environmental conditions (drying-wetting cycles) in Mediterranean landscapes, implying potential impacts on ecosystem functioning and our ability to predict soil response to environmental shifts. Using nitrogen mineralization rate (NMR) as a representative function we document highly variable NMR over the sampling years, land uses and soil depths and lack of significant associations with the monitored environmental variables and individual taxa. In summary, our study provides novel insights on the organization and functioning of microbial communities at Mediterranean ecosystems and sets directions towards a more advanced understanding of the relationships among environmental factors, microbial community structure, and ecosystem functioning that could contribute to sustainable management of these severely degraded ecosystems.
Evolutionary rates are correlated between cockroach symbiont and mitochondrial genomes
Authors: Arab Daej A. , Bourguignon Thomas , Wang Zongqing , Ho Simon Y. W. , Lo Nathan 
Published: February 2019

AbstractBacterial endosymbionts evolve under strong host-driven selection. Factors influencing host evolution might affect symbionts in similar ways, potentially leading to correlations between the molecular evolutionary rates of hosts and symbionts. Although there is evidence of rate correlations between mitochondrial and nuclear genes, similar investigations of hosts and symbionts are lacking. Here we demonstrate a correlation in molecular rates between the genomes of an endosymbiont (Blattabacterium cuenoti) and the mitochondrial genomes of their hosts (cockroaches). We used partial genome data for multiple strains of B. cuenoti to compare phylogenetic relationships and evolutionary rates for 55 cockroach/symbiont pairs. The phylogenies inferred for B. cuenoti and the mitochondrial genomes of their hosts were largely congruent, as expected from their identical maternal and cytoplasmic mode of inheritance. We found a correlation between evolutionary rates of the two genomes, based on comparisons of root-to-tip distances and on comparisons of the branch lengths of phylogenetically independent species pairs. Our results underscore the profound effects that long-term symbiosis can have on the biology of each symbiotic partner.
Auxin export from proximal fruits drives arrest in competent inflorescence meristems
Authors: Ware Alexander , Walker Catriona H. , Šimura Jan , Ljung Karin , Bishopp Anthony , Wilson Zoe , Bennett Tom 
Published: February 2019

ABSTRACTA well-defined set of regulatory pathways control entry into the reproductive phase in flowering plants [1]. Conversely, little is known about the mechanisms that control the end of the reproductive phase (‘floral arrest’), despite this being a critical process for optimising fruit and seed production. Complete fruit removal or lack of fertile fruit-set in male sterile mutants, for example male sterile1 (ms1), prevents timely floral arrest in the model plant Arabidopsis [2]. These observations formed the basis for Hensel and colleagues’ model in which end-of-flowering was proposed to result from a cumulative fruit/seed-derived signal that caused simultaneous ‘global proliferative arrest’ (GPA) in all inflorescences [2]. Recent studies have suggested that end-of-flowering involves gene expression changes at the floral meristem which are at least in part controlled by the FRUITFULL-APETELA2 pathway [3,4], however there is limited understanding of how this process is controlled and the communication needed at the whole plant level. Here, we provide new information providing a framework for the fruit-to-meristem (F-M) communication implied by the GPA model [5]. We show that floral arrest in Arabidopsis is not ‘global’ and does not occur synchronously between branches, but rather that the arrest of each inflorescence is a local process, driven by auxin export from fruit proximal to the inflorescence meristem (IM). Furthermore, we show that inflorescence meristems are only competent for floral arrest once they reach a certain developmental age. Understanding the regulation of floral arrest is of major importance for the future manipulation of flowering to extend and maximise crop yields.
A proposed microcosm for landscape ecology – beyond the binary to the patch-mosaic model
Authors: Wiersma Yolanda F. , Wigle Rachel D. , McMullin R. Troy 
Published: February 2019

AbstractBackgroundMicrocosms such as pitcher plants, or patches of mosses on a rock surface, have been used worldwide to allow for manipulative experiments that test hypotheses for patterns observed at larger extents, such as dispersal or community assemblage. Such microcosms can also be applied to questions in landscape ecology, but are limited by their binary (patch/non-patch structure). Here we examine a more realistic model landscape system that shares the patch-mosaic structure common to kilometres-extent landscapes. This system of lichen thalli on tree trunks has been shown to have consistent spatial patterns across replicate microcosms, but only when sampling within a limited area. To be relevant for experimentation across scales, it is necessary to determine whether previously observed patterns are consistent when sampling across a broader region and when using different tree species. Here, we test for consistent landscape patch pattern in both maco- and micro-lichens across 21 balsam fir (Abies balsamea) and yellow birch (Betula alleghaniensis) trees.MethodsWe measured spatial pattern of lichen thalli along the trunks of two species of trees, at two spatial resolutions; trees within a single stand (∼100 × 50 m) and trees dispersed across a larger region (500 km2). We used a “lichen ladder” comprised of 5 10 × 10 cm sampling blocks to quantify number of species and individuals in a 50 cm section of the tree trunk. We tested for similar patterns along the trunk and between the north and south sides at both sampling intensities using perMANOVA.ResultsWe find that lichen patches on tree trunks can function as replicate microscoms for landscape ecology. Patterns of thalli along the trunks of trees and between the north and south aspects of the trunk are statistically significantly consistent, although there is variation between tree species, and groups of lichens included. Our microcosm could be used as a model system for landscape ecology research; but researchers should test for consistent patterns first.
The U125 insertion device beamline at the Metrology Light Source
Authors: Gottwald Alexander , Kaser Hendrik , Kolbe Michael 
Published: February 2019

At the Metrology Light Source, an electron storage ring dedicated to metrological applications, the U125 insertion device beamline utilizes undulator radiation for various applications over a broad spectral range. Using a hybrid normal-incidence and grazing-incidence in-vacuum switchable plane-grating monochromator, a spectral region ranging from the near-infrared to soft X-ray is covered. The beamline is dedicated to surface-analytical methods, e.g. ellipsometry, photoelectron spectroscopy or photoemission tomography. The traceability of radiometric quantities, i.e. quantitative determination of the available radiant power (or photon flux), is required for some of these applications to support the metrological aspect of the measurements. In particular, attention is paid to the suppression of unwanted spectral contributions from higher diffraction orders, and to the monitoring of the radiation intensity during the measurements. With the results from the beamline commissioning, an uncertainty budget for all relevant radiometric quantities was established.
Red capital in Hong Kong
Authors: Wang-Kaeding Heidi , Kaeding Malte Philipp 
Published: February 2019

PurposeThe purpose of this paper is threefold: first, to recount the scale, composition and agents of red capital in Hong Kong; second, to conceptualise the peculiarity of red capital; and third, to explore the impact of red capital on the political and economic institutional setup in Hong Kong.Design/methodology/approachThe paper consults the comparative capitalism literature to conceptualise the phenomenon of red capital. The paper gathers data from Hong Kong Stock Exchange and indices to provide an overview of red capital. Furthermore, the case study of 2016 Legislative Election is deployed to investigate the mechanisms of red capital’s influence. The paper concludes with a summary of how red capital may challenge the validity of the “One Country, Two Systems” framework.FindingsThis paper argues that red capital replicates China’s state–capital nexus in Hong Kong and morphs the game of competition in favour of Chinese nationally controlled companies. In tandem with the emerging visibility of the party–state in Hong Kong’s economic sphere, the authors observe attempts of Chinese economic actors to compromise democratic institutions, deemed obstacles to state control.Originality/valueThis paper is the first attempt to systematically embed the discussion of red capital into comparative capitalism literature. This study provides conceptual tools to examine why red capital could pose a threat to liberal societies such as Hong Kong. Through this paper, we introduce a novel research agenda to scrutinise capital from authoritarian states and investigate how the capital is changing the political infrastructure shaped by liberal principles and values.
Volunteer educational initiative for undocumented immigrants’ children
Authors: Murthy Venkatesh 
Published: February 2019

Learning outcomes
The learning outcomes are as follows: to gain insights into an immigrant community with an emphasis on positioning stakeholders using power, legitimacy and urgency constructs; to help participants dwell on a decision-making process under challenging circumstances; and to help learners understand the level of commitment and efforts needed in initiating and sustaining a volunteer initiative. At the micro level, the case helps learners understand the nature of an interaction between two distinct social groups (ragpickers and volunteers). At the macro level, the case helps the learners understand the way marginalised migratory communities think and behave in the larger scheme of politics, religion and ever-increasing migration at the global level.

Case overview/synopsis
This case is about an informal educational activity initiated by a group of volunteers who intend to eradicate illiteracy amongst ragpickers’ children in Rohtak, a small city in Haryana, India. This town has a population of <0.4 million and houses several immigrant families who come from different regions of India. Most immigrant families are into construction and rag picking. The localites mostly perceive ragpickers as undocumented immigrants from Bangladesh. Usually, most ragpickers’ children engage in garbage collection and do not attend school. In this backdrop, a group led by Mohan set up an evening class in an open ground, which in turn attracted several children from both the ragpicker and local communities alike. However, after a few days, the harsh weather made the volunteer team to shift the classes to a closed room. The shifting from the open ground to the closed room infuriated the parents and resulted in the parents not allowing their children to go to school. In this context, the volunteer team has to decide whether to continue the voluntary school or shut it down.

Complexity academic level
Executive, Under-Graduation and Post Graduation

Supplementary materials
Teaching Notes are available for educators only. Please contact your library to gain login details or email support@emeraldinsight.com to request teaching notes.

Subject code
CSS 7: Management Science