Quantitative Comparison of Abundance Structures of Generalized Communities: From B-Cell Receptor Repertoires to Microbiomes

The \emph{community}, the assemblage of organisms co-existing in a given space and time, has the potential to become one of the unifying concepts of biology, especially with the advent of high-throughput sequencing experiments that reveal genetic diversity exhaustively. In this spirit we show that a tool from community ecology, the Rank Abundance Distribution (RAD), can be turned by the new MaxRank normalization method into a generic, expressive descriptor for quantitative comparison of communities in many areas of biology. To illustrate the versatility of the method, we analyze RADs from various \emph{generalized communities}, i.e.\ assemblages of genetically diverse cells or organisms, including human B cells, gut microbiomes under antibiotic treatment and of different ages and countries of origin, and other human and environmental microbial communities. We show that normalized RADs enable novel quantitative approaches that help to understand structures and dynamics of complex generalize communities

Firewood residential heating – local versus remote influence on the aerosol burden

We report the first-time use of the Lagrangian particle dispersion model (LPDM) FLEXPART to simulate isotope ratios of the biomass burning tracer levoglucosan. Here, we combine the model results with observed levoglucosan concentrations and δ13C to assess the contribution of local vs. remote emissions from firewood domestic heating to the particulate matter sampled during the cold season at two measurements stations of the Environmental Agency of North Rhine-Westphalia, Germany.For the investigated samples, the simulations indicate that the largest part of the sampled aerosol is 1 to 2 d old and thus originates from local to regional sources. Consequently, ageing, also limited by the reduced photochemical activity in the dark cold season, has a minor influence on the observed levoglucosan concentration and δ13C. The retro plume ages agree well with those derived from observed δ13C (the “isotopic” ages), demonstrating that the limitation of backwards calculations to 7 d for this study does not introduce any significant bias. A linear regression analysis applied to the experimental levoglucosan δ13C vs. the inverse concentration confirms the young age of aerosol. The high variability in the observed δ13C implies that the local levoglucosan emissions are characterized by different isotopic ratios in the range of −26.3 ‰ to −21.3 ‰. These values are in good agreement with previous studies on levoglucosan source-specific isotopic composition in biomass burning aerosol. Comparison between measured and estimated levoglucosan concentrations suggests that emissions are underestimated by a factor of 2 on average. These findings demonstrate that the aerosol burden from home heating in residential areas is not of remote origin. In this work we show that combining Lagrangian modelling with isotope ratios is valuable to obtain additional insight into source apportionment. Error analysis shows that the largest source of uncertainty is limited information on isotope ratios of levoglucosan emissions. Based on the observed low extent of photochemical processing during the cold season, levoglucosan can be used under similar conditions as a conservative tracer without introducing substantial bias

Benchmarking source specific isotopic ratios of levoglucosan to better constrain the contribution of domestic heating to the air pollution

We report source specific isotope ratios of levoglucosan, the specific biomass burning tracer, in aerosol particle from the combustion of selected woods used for domestic heating in Europe, of coals containing cellulose (lignites) as well as of corn, a C4 plant. Here, we combine compound specific δ13C measurements of levoglucosan with total carbon δ13C of parent materials, to assess isotopic fractionations due to biosynthetic pathways or combustion processes. Levoglucosan formed during the combustion of cellulose from coals shows with δ13C of −21.1‰ and −18.6‰ a moderate enrichment in the heavier isotope compared to the C3 plant samples. Contrarily, observed levoglucosan isotope ratios of −25.0 to −21.5‰ for C3 plant samples are significantly lower than for the C4 plant sample (−12.4‰), as expected from the stronger 13C discrimination during the carbon fixation process by C3 compared to C4 plants. Overall, the C4 plant sample shows a 13C enrichment in all bulk measurements, on average by 12.2‰, 14.2‰ and 14.2‰ for total carbon (TC) in aerosol particle, whole plant/coal material and cellulose samples, respectively. Further, δ13C measurements of levoglucosan and TC of biomass burning aerosol particles, bulk plant/coal and cellulose in C3 plant samples agree well with the published observations. The combined levoglucosan/TC isotopic analyses can be used to differentiate among C3/coal/C4 origin of the smoke emissions from the cellulose-containing-fuel combustion. Noticeably, there is a consistent δ13C offset between C3 plant material and levoglucosan, which allows deriving emission levoglucosan isotope ratios when the combusted plant types are known

Molecular composition of the human primary visual cortex profiled by multimodal mass spectrometry imaging

The primary visual cortex (area V1) is an extensively studied part of the cerebral cortex with well-characterized connectivity, cellular and molecular architecture and functions (for recent reviews see Amunts and Zilles, Neuron 88:1086–1107, 2015; Casagrande and Xu, Parallel visual pathways: a comparative perspective. The visual neurosciences, MIT Press, Cambridge, pp 494–506, 2004). In humans, V1 is defined by heavily myelinated fibers arriving from the radiatio optica that form the Gennari stripe in cortical layer IV, which is further subdivided into laminae IVa, IVb, IVcα and IVcβ. Due to this unique laminar pattern, V1 represents an excellent region to test whether multimodal mass spectrometric imaging could reveal novel biomolecular markers for a functionally relevant parcellation of the human cerebral cortex. Here we analyzed histological sections of three post-mortem brains with matrix-assisted laser desorption/ionization mass spectrometry imaging and laser ablation inductively coupled plasma mass spectrometry imaging to investigate the distribution of lipids, proteins and metals in human V1. We identified 71 peptides of 13 different proteins by in situ tandem mass spectrometry, of which 5 proteins show a differential laminar distribution pattern revealing the border between V1 and V2. High-accuracy mass measurements identified 123 lipid species, including glycerolipids, glycerophospholipids and sphingolipids, of which at least 20 showed differential distribution within V1 and V2. Specific lipids labeled not only myelinated layer IVb, but also IVa and especially IVc in a layer-specific manner, but also and clearly separated V1 from V2. Elemental imaging further showed a specific accumulation of copper in layer IV. In conclusion, multimodal mass spectrometry imaging identified novel biomolecular and elemental markers with specific laminar and inter-areal differences. We conclude that mass spectrometry imaging provides a promising new approach toward multimodal, molecule-based cortical parcellation

PET/MRI enables simultaneous in vivo quantification of β-cell mass and function

Non-invasive imaging of β-cells represents a desirable preclinical and clinical tool to monitor the change of β-cell mass and the loss of function during pre-diabetic stages. Although it is widely accepted that manganese (Mn) ions are actively gated by voltage-dependent calcium channels (VDCC) in response to glucose metabolism, little is known on its specificity in vivo for quantification of islet β-cell function using Mn and magnetic resonance imaging (MRI). On the other hand, glucagon-like-peptide-1 receptor (GLP-1R) represents a validated target for the estimation of β-cell mass using radiolabeled exendin-4 (Ex4) and positron emission tomography (PET). However, a multiparametric imaging workflow revealing β-cell mass and function quantitatively is still missing

Firewood residential heating - local versus regional influence on the aerosol burden

As a particular form of biomass burning (BB), domesticheating with firewood is a major source of fine dust inthe cold season. Understanding its impact on air qualityrequires reliable aerosol source apportionment andassessment of prevailing loss processes. Further, to establisheffective mitigation policies, it is necessary toaccurately quantify the contribution of local vs. remotesources to the aerosol burden. To this end, source-receptormodelling is employed, such as chemical massbalance or Lagrangian techniques, to calculate concentrationsof the BB specific tracer in aerosol, levoglucosan(Fine et al. 2002, Chunmao et al. 2019). In the lastdecades, it has been shown that combining stable isotoperatios with concentration measurements allows forseparating the impact of chemical degradation fromchanges linked to source strength or atmospherictransport. Based on that, Gensch et al. (2018) developeda numerical approach, comparing stable carbonisotopic ratio and concentration measurements withback trajectory analyses by the Lagrangian particle dispersionmodel FLEXPART (https://www.flexpart.eu/) toinvestigate chemical aging processes in BB aerosol.In the present study, stable carbon isotopes were implementedin the full dispersed output of FLEXPART byexplicitly tracking of the levoglucosan fraction containing13C. Further, sensitivity studies were carried out toexamine the simulation responses to the uncertaintiesof the governing atmospheric processes described inFLEXPART and thus, to determine the model performancefor given conditions. Finally, the set of selectedmodelling routines were applied in a case study with thegoal to assess the contribution of local vs. remotesources of biomass burning emissions from residentialheating to the particulate matter sampled at twomeasurement stations of the North Rhine-WestphaliaEnvironmental Agency, LANUV. Thereby, the measuredlevoglucosan concentration and isotopic composition in50 selected aerosol samples taken at an urbanbackground station in Mülheim-Styrum and at a ruralbackground station in the Eifel, in the cold seasons of2015 - 2017 were compared with the model results.The simulations indicate that the biggest fraction of thesampled aerosol is 1 to 2 days old. Chemical aging, alsolimited by low mean OH concentrations in the cold season,has thus a minor influence on the observedlevoglucosan concentration and δ13C (Fig. 1). Theexperimental data, interpreted as a two end-membermixing series between low-concentration/isotopicallyheavyback-ground and high-concentration/isotopicallylightfresh emissions, support the model outcome,showing similar isotopic ratios for the two constituents.The high variability in the observed δ13C implies that thelocal levoglucosan emissions are characterized by verydifferent isotopic ratios in the range of -25.3 to -21.4 %(Fig. 1 in Pdf). These values are in good agreement withprevious studies on levoglucosan source specificisotopic composition in BB aerosol (Sang et al. 2012).These findings demonstrate that the aerosol burdenfrom residential heating in living areas is of local originand thus, mitigation is possible through reduction oflocal emissions. In this work we show that combiningLagrangian modelling with isotope ratios is valuable toobtain additional insight in source apportionment.There is, though, a need for a better isotopic descriptionof sources. Moreover, studies investigating long rangetransport of BB aerosol from large-scale fires in the dryseason are essential to examine the role of aging amongother loss processes.Fine, P.M., Cass, G.R. and Simoneit, B.R.T. (2002) J. Geophys.Res., [Atmos.], doi 10.1029/2001jd000661Chunmao, Z., Yugo, K., et al. (2019) Environ. Pollut., doi10.1016/j.envpol.2019.01.003Gensch, I., Sang, X.F., et al. (2018) Environ. Sci.&Tech.,doi 10.1021/acs.est.8b03054Sang, X.F., Gensch, I., et al. (2012) Environ. Sci.&Tech.,doi 10.1021/ es204094

Broken stick distribution (solid line) and NRADs of <i>IgG</i>⁺<i>CD</i>27⁺ fractions (points).

<p>Inset: section of hierarchical clustering dendrogram where broken stick distribution appears. This plot adopts the usual presentation of the broken stick distribution in the literature with linear horizontal axis and logarithmic vertical axis. Therefore the boomerang shapes of the log-log <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1005362#pcbi.1005362.g004" target="_blank">Fig 4</a> appear horizontally stretched.</p

Rank abundance distributions of memory B cell receptors.

<p>Four different B cell receptor sub-classes from donors 1 (replicate samples A, B) and 2 (replicates C, D) are compared. Top left panel: Log-log plot of RADs prior to normalization. Top right: Log-log plot of corresponding NRADs. Legend for RADs and NRADs is given in bottom right panel. Bottom left: Hierarchical clustering tree based on all pairwise distances between the 16 NRADs.</p

GlobalPatterns dataset.

<p>(A) Hierarchical clustering dendrogram based on distances between NRADs. (B) NRADs of three samples of similar origin that form a cluster. (C) Microbiome of human palm of human individual 1 clusters closely with sediments 2 and 3, but is more distant to tongue microbiome of individual 1. (D) Three differently shaped NRADs with same entropy.</p

Diversity of the <i>V</i>_<i>H</i> region of BCRs.

<p>(A) The human genome contains sets of <i>V</i>_<i>H</i>, <i>D</i>_<i>H</i>, and <i>J</i>_<i>H</i> gene segments. (B) The “variable” <i>V</i>_<i>H</i> segments can be grouped into seven <i>V</i>_<i>H</i> families based on sequence similarity. (C) A genetically diverse pool of B cells is generated by V(D)J recombination. (D) Exposure to antigens induces an adaptation of the BCR repertoire, generating genetic variants and changing the usage pattern of <i>V</i>_<i>H</i> gene segments.</p