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A hump-backed trend in bacterial diversity with elevation on Mount Fuji, Japan.
Singh, Dharmesh,Takahashi, Koichi,Kim, Mincheol,Chun, Jongsik,Adams, Jonathan M Springer-Verlag 2012 Microbial ecology Vol.63 No.2
<P>Little is known of how bacterial diversity in soils varies with elevation. One previous study found a decline with elevation, whereas another found no trend. We chose Mount Fuji of Japan as a geologically and topographically simple mountain system. Samples were taken at elevational intervals, between the base of the mountain at 1,000 m and its summit at 3,700 m. Polymerase chain reaction-amplified soil DNA for the bacterial 16S gene targeting V1-V3 region was pyrosequenced using the 454 Roche machine, and taxonomically classified with reference to a bioinformatic database. There was a significant 'peak' in total bacterial diversity at around 2,500 m above the tree line with a decline towards the highest elevations around 3,700 m near the summit. Individual bacterial phyla show distinct trends-increase, decrease, or a mid-elevational 'bulge' in diversity. Bacterial diversity does not parallel woody plant or herbaceous plant diversity. We suggest that beyond the tree and vegetation line, the more extreme temperature fluctuations, stronger UV, lack of nutrients, and more frequent disturbance of the loose substrate of these slopes allows less competition and greater bacterial species diversity due to 'lottery' recruitment. However, at the highest elevations, the physiological challenges are so extreme that fewer bacterial species are capable of surviving.</P>
Are tropical butterflies more colorful?
Adams, Jonathan M.,Kang, Changku,June‐,Wells, Mark Springer Japan 2014 Ecological research Vol.29 No.4
<P><B>Abstract</B></P><P>There is a common and long‐standing belief that tropical butterflies are more striking in their coloration than those of cooler climates. It has been suggested that this is due to more intense biotic selection or mate selection in the tropics. We tested whether there were differences in coloration by examining the dorsal surface color properties of male butterflies from three regions of the western hemisphere: the Jatun‐Satcha Reserve in lowland Ecuador (tropical), the state of Florida, USA (subtropical) and the state of Maine, USA (cool temperate). We digitally photographed the dorsal wing and body surface of male butterfly specimens from Maine, Florida, and Ecuador. For each photograph, we analyzed the mean and variation for the color‐parameters that are thought to be related to colorfulness; namely Hue, saturation and intensity. Overall, the Ecuadorian sample exhibited more varied intensity, saturation, and Hue compared to the other regions. These results suggest a more complex assemblage of colors and patterns regionally and on a butterfly‐by‐butterfly basis in the tropics. The greater complexity of colors within each butterfly in our Ecuadorian sample suggests that tropical butterflies are indeed more ‘colorful’, at least by some measures. Possible reasons for this include stronger predation pressure selecting for aposematism, greater species diversity selecting for camouflage or warning coloration against potential predators, and easier recognition of potential mates in a species rich environment.</P>
Adam M. Greenbaum,Jonathan R. Fromm,Ajay K. Gopal,A. McGarry Houghton 대한혈액학회 2022 Blood Research Vol.57 No.2
Background B-cell non-Hodgkin lymphomas (NHL) are hematologic malignancies that arise in the lymph node. Despite this, the malignant cells are not cleared by the immune cells present. The failure of anti-tumor immunity may be due to immune checkpoints such as the PD-1/PDL-1 axis, which can cause T-cell exhaustion. Unfortunately, unlike Hodgkin lymphoma, checkpoint blockade in NHL has shown limited efficacy. Methods We performed an extensive functional analysis of malignant and non-malignant lymph nodes using high dimensional flow cytometry. We compared follicular lymphoma (FL), diffuse large B-cell lymphoma (DLBCL), and lymph nodes harboring reactive hyperplasia (RH). Results We identified an expansion of CD8+PD1+ T-cells in the lymphomas relative to RH. Moreover, we demonstrate that these cells represent a mixture of activated and exhausted T-cells in FL. In contrast, these cells are nearly universally activated and functional in DLBCL. This is despite expression of counter-regulatory molecules such as PD-1, TIM-3, and CTLA-4, and the presence of regulatory T-cells. Conclusion These data may explain the failure of single-agent immune checkpoint inhibitors in the treatment of DLBCL. Accordingly, functional differences of CD8+ T-cells between FL and DLBCL may inform future therapeutic targeting strategies.
Skelton, Jonathan M.,Burton, Lee A.,Jackson, Adam J.,Oba, Fumiyasu,Parker, Stephen C.,Walsh, Aron Royal Society of Chemistry 2017 Physical chemistry chemical physics Vol.19 No.19
<▼1><P>First-principles lattice-dynamics calculations are used to model and compare the vibrational spectra and thermal transport of four bulk tin-sulphide materials.</P></▼1><▼2><P>We present an in-depth first-principles study of the lattice dynamics of the tin sulphides SnS<SUB>2</SUB>, <I>Pnma</I> and π-cubic SnS and Sn<SUB>2</SUB>S<SUB>3</SUB>. An analysis of the harmonic phonon dispersion and vibrational density of states reveals phonon bandgaps between low- and high-frequency modes consisting of Sn and S motion, respectively, and evidences a bond-strength hierarchy in the low-dimensional SnS<SUB>2</SUB>, <I>Pnma</I> SnS and Sn<SUB>2</SUB>S<SUB>3</SUB> crystals. We model and perform a complete characterisation of the infrared and Raman spectra, including temperature-dependent anharmonic linewidths calculated using many-body perturbation theory. We illustrate how vibrational spectroscopy could be used to identify and characterise phase impurities in tin sulphide samples. The spectral linewidths are used to model the thermal transport, and the calculations indicate that the low-dimensional Sn<SUB>2</SUB>S<SUB>3</SUB> has a very low lattice thermal conductivity, potentially giving it superior performance to SnS as a candidate thermoelectric material.</P></▼2>
Tropical Soil Bacterial Communities in Malaysia: pH Dominates in the Equatorial Tropics Too
Tripathi, Binu M.,Kim, Mincheol,Singh, Dharmesh,Lee-Cruz, Larisa,Lai-Hoe, Ang,Ainuddin, A. N.,Go, Rusea,Rahim, Raha Abdul,Husni, M. H. A.,Chun, Jongsik,Adams, Jonathan M. Springer-Verlag 2012 Microbial ecology Vol.64 No.2
Soil pH mediates the balance between stochastic and deterministic assembly of bacteria
Tripathi, Binu M.,Stegen, James C.,Kim, Mincheol,Dong, Ke,Adams, Jonathan M.,Lee, Yoo Kyung Nature Publishing Group UK 2018 The ISME journal Vol.12 No.4
<P>Little is known about the factors affecting the relative influences of stochastic and deterministic processes that govern the assembly of microbial communities in successional soils. Here, we conducted a meta-analysis of bacterial communities using six different successional soil datasets distributed across different regions. Different relationships between pH and successional age across these datasets allowed us to separate the influences of successional age (i.e., time) from soil pH. We found that extreme acidic or alkaline pH conditions lead to assembly of phylogenetically more clustered bacterial communities through deterministic processes, whereas pH conditions close to neutral lead to phylogenetically less clustered bacterial communities with more stochasticity. We suggest that the influence of pH, rather than successional age, is the main driving force in producing trends in phylogenetic assembly of bacteria, and that pH also influences the relative balance of stochastic and deterministic processes along successional soils. Given that pH had a much stronger association with community assembly than did successional age, we evaluated whether the inferred influence of pH was maintained when studying globally distributed samples collected without regard for successional age. This dataset confirmed the strong influence of pH, suggesting that the influence of soil pH on community assembly processes occurs globally. Extreme pH conditions likely exert more stringent limits on survival and fitness, imposing strong selective pressures through ecological and evolutionary time. Taken together, these findings suggest that the degree to which stochastic vs. deterministic processes shape soil bacterial community assembly is a consequence of soil pH rather than successional age.</P>
Ousaka, Naoki,Grunder, Sergio,Castilla, Ana M.,Whalley, Adam C.,Stoddart, J. Fraser,Nitschke, Jonathan R. American Chemical Society 2012 JOURNAL OF THE AMERICAN CHEMICAL SOCIETY - Vol.134 No.37
<P>A series of large, optically active Fe<SUB>4</SUB>L<SUB>6</SUB> cages was prepared from linear 5,5′-bis(2-formylpyridines) incorporating varying numbers (<I>n</I> = 0–3) of oligo-<I>p</I>-xylene spacers, chiral amines, and Fe<SUP>II</SUP>. When a cage was constructed from the ligand bridged by one <I>p</I>-xylene spacer (<I>n</I> = 1) and a bulky chiral amine, both a homochiral Fe<SUB>2</SUB>L<SUB>3</SUB> helicate and Fe<SUB>4</SUB>L<SUB>6</SUB> cage were observed to coexist in solution due to a delicate balance between steric factors. In contrast, when a less bulky chiral amine was used, only the Fe<SUB>4</SUB>L<SUB>6</SUB> cage was observed. In the case of larger cages (<I>n</I> = 2, 3), long-range (>2 nm) stereochemical coupling between metal centers was observed, which was minimally diminished as the ligands were lengthened. This communication was mediated by the ligands’ geometries and rigidity, as opposed to gearing effects between xylene methyl groups: the metal-centered stereochemistry was not observed to affect the axial stereochemistry of the ligands.</P><P><B>Graphic Abstract</B> <IMG SRC='http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/jacsat/2012/jacsat.2012.134.issue-37/ja306615d/production/images/medium/ja-2012-06615d_0014.gif'></P><P><A href='http://pubs.acs.org/doi/suppl/10.1021/ja306615d'>ACS Electronic Supporting Info</A></P>
Towards a Comprehensive Catalog of Zebrafish Behavior 1.0 and Beyond
Kalueff, Allan V.,Gebhardt, Michael,Stewart, Adam Michael,Cachat, Jonathan M.,Brimmer, Mallorie,Chawla, Jonathan S.,Craddock, Cassandra,Kyzar, Evan J.,Roth, Andrew,Landsman, Samuel,Gaikwad, Siddharth Mary Ann Liebert 2013 Zebrafish Vol.10 No.1