41 research outputs found
Data_Sheet_1_Semen Microbiome Biogeography: An Analysis Based on a Chinese Population Study.PDF
Investigating inter-subject heterogeneity (or spatial distribution) of human semen microbiome diversity is of important significance. Theoretically, the spatial distribution of biodiversity constitutes the core of microbiome biogeography. Practically, the inter-subject heterogeneity is crucial for understanding the normal (healthy) flora of semen microbiotas as well as their possible changes associated with abnormal fertility. In this article, we analyze the scaling (changes) of semen microbiome diversity across individuals with DAR (diversity-area relationship) analysis, a recent extension to classic SAR (species-area relationship) law in biogeography and ecology. Specifically, the unit of âareaâ is individual subject, and the microbial diversity in seminal fluid of an individual (area) is assessed via metagenomic DNA sequencing technique and measured in the Hill numbers. The DAR models were then fitted to the accrued diversity across different number of individuals (area size). We further tested the difference in DAR parameters among the healthy, subnormal, and abnormal microbiome samples in terms of their fertility status based on a cross-sectional study of a Chinese cohort. Given that no statistically significant differences in the DAR parameters were detected among the three groups, we built unified DAR models for semen microbiome by combining the healthy, subnormal, and abnormal groups. The model parameters were used to (i) estimate the microbiome diversity scaling in a population (cohort), and construct the so-termed DAR profile; (ii) predict/construct the maximal accrual diversity (MAD) profile in a population; (iii) estimate the pair-wise diversity overlap (PDO) between two individuals and construct the PDO profile; (iv) assess the ratio of individual diversity to population (RIP) accrual diversity. The last item (RIP) is a new concept we propose in this study, which is essentially a ratio of local diversity to regional or global diversity (LRD/LGD), applicable to general biodiversity investigation beyond human microbiome.</p
Data_Sheet_2_Assessing and Interpreting the Within-Body Biogeography of Human Microbiome Diversity.xls
<p>A human body hosts a relatively independent microbiome including five major regional biomes (i.e., airway, oral, gut, skin, and urogenital). Each of them may possess different regional characteristics with important implications to our health and diseases (i.e., so-termed microbiome associated diseases). Nevertheless, these regional microbiomes are connected with each other through diffusions and migrations. Here, we investigate the within-body (intra-individual) distribution feature of microbiome diversity via diversity area relationship (DAR) modeling, which, to the best of our knowledge, has not been systematically studied previously. We utilized the Hill numbers for measuring alpha and beta-diversities and built 1,200 within-body DAR models with to date the most comprehensive human microbiome datasets of 18 sites from the human microbiome project (HMP) cohort. We established the intra-DAR profile (z-q pattern: the diversity scaling parameter z of the power law (PL) at diversity order q = 0â3), intra-PDO (pair-wise diversity overlap) profile (g-q), and intra-MAD (maximal accrual diversity) profile (D<sub>max</sub>-q) for the within-body biogeography of the human microbiome. These profiles constitute the âmapsâ of the within-body biogeography, and offer important insights on the within-body distribution of the human microbiome. Furthermore, we investigated the heterogeneity among individuals in their biogeography parameters and found that there is not an âaverage Joeâ that can represent majority of individuals in a cohort or population. For example, we found that most individuals in the HMP cohort have relatively lower maximal accrual diversity (MAD) or in the âlong tailâ of the so-termed power law distribution. In the meantime, there are a small number of individuals in the cohort who possess disproportionally higher MAD values. These findings may have important implications for personalized medicine of the human microbiome associated diseases in practice, besides their theoretical significance in microbiome research such as establishing the baseline for the conservation of human microbiome.</p
Data_Sheet_1_Assessing and Interpreting the Within-Body Biogeography of Human Microbiome Diversity.PDF
<p>A human body hosts a relatively independent microbiome including five major regional biomes (i.e., airway, oral, gut, skin, and urogenital). Each of them may possess different regional characteristics with important implications to our health and diseases (i.e., so-termed microbiome associated diseases). Nevertheless, these regional microbiomes are connected with each other through diffusions and migrations. Here, we investigate the within-body (intra-individual) distribution feature of microbiome diversity via diversity area relationship (DAR) modeling, which, to the best of our knowledge, has not been systematically studied previously. We utilized the Hill numbers for measuring alpha and beta-diversities and built 1,200 within-body DAR models with to date the most comprehensive human microbiome datasets of 18 sites from the human microbiome project (HMP) cohort. We established the intra-DAR profile (z-q pattern: the diversity scaling parameter z of the power law (PL) at diversity order q = 0â3), intra-PDO (pair-wise diversity overlap) profile (g-q), and intra-MAD (maximal accrual diversity) profile (D<sub>max</sub>-q) for the within-body biogeography of the human microbiome. These profiles constitute the âmapsâ of the within-body biogeography, and offer important insights on the within-body distribution of the human microbiome. Furthermore, we investigated the heterogeneity among individuals in their biogeography parameters and found that there is not an âaverage Joeâ that can represent majority of individuals in a cohort or population. For example, we found that most individuals in the HMP cohort have relatively lower maximal accrual diversity (MAD) or in the âlong tailâ of the so-termed power law distribution. In the meantime, there are a small number of individuals in the cohort who possess disproportionally higher MAD values. These findings may have important implications for personalized medicine of the human microbiome associated diseases in practice, besides their theoretical significance in microbiome research such as establishing the baseline for the conservation of human microbiome.</p
Linearâ, Cyclicâ, and Multiblock Amphiphilic Polyelectrolytes as Surfactants in Emulsion Polymerization: Role of Topological Structure
Combining
atom transfer radical polymerization (ATRP) and âclickâ
chemistry, a set of well-defined amphiphilic block copolymers polyÂ(<i>n</i>-butyl acrylate)-<i>b</i>-polyÂ(acrylic acid)
(P<i>n</i>BA<sub>20</sub>-PAA<sub>85</sub>) with a similar
chemical component, but different topological structures, i.e., <i>linear-</i>, <i>cyclic-</i>, and <i>multiblock</i> structures, were successfully prepared, characterized (size exclusion
chromatography (SEC), FT-IR and <sup>1</sup>H NMR), and used as surfactants
in emulsion polymerization. Our further transmission electron microscopy
(TEM) and laser light scattering (LLS) characterization of the resultant
latex particles demonstrates all the surfactants with different topologies
can effectively stabilize the latex particles but no significant difference
among the solids contents was observed. Moreover, we have, <i>for the first time</i>, experimentally established the quantitative
relation between the final number of latex particles (<i>N</i><sub>p</sub>) and the concentration of polymeric surfactant with
different topologies (<i>C</i>), i.e., <i>N</i><sub>p</sub> = <i>kC</i><sup>α</sup>, and the order
of our measured exponent α is as follows: α<sub>multi</sub>(1.10) > α<sub>linear</sub>(0.81) ℠α<sub>cyclic</sub>(0.73), indicating cyclic surfactant molecules behave more like small-molecule
surfactants attributed to its strongest unimers extraction and diffusion
ability; in contrast, multiblock surfactant molecules can act as seeds
to directly nucleate to create latex particles. In addition, <i>N</i><sub>p,multi</sub> > <i>N</i><sub>p,linear</sub> â„ <i>N</i><sub>p,cyclic</sub> at higher concentration,
and <i>N</i><sub>p,linear</sub> > <i>N</i><sub>p,cyclic</sub> â„ <i>N</i><sub>p,multi</sub> at lower
concentration was observed. Similar results (α<sub>multi</sub>(1.02) > α<sub>linear</sub>(0.65) ℠α<sub>cyclic</sub>(0.58)) were also observed when polystyrene-<i>b</i>-polyÂ(acrylic
acid) (PS<sub>9</sub>âPAA<sub>60</sub>) copolymers were used
as surfactants. Further aqueous SEC characterization shows the broad
size distribution of our micellar solution has no effect on obtaining
narrowly distributed latex particles. Finally, interfacial tension
measurement of the micellar solution indicates, compared to multiblock
structure, the rate of adsorption at a hydrophobic interface is much
faster for linear and cyclic-block structures, agreeing with our observed
order of exponent α
Self-Assembly Assisted Polypolymerization (SAAP) of Diblock Copolymer Chains with Two Reactive Groups at Its Insoluble End
Preparation of diblock copolymers,
(âĄ,N<sub>3</sub>)-polyÂ(<i>N</i>-isopropylacrylamide)-<i>b</i>-polyÂ(<i>N</i>,<i>N</i>-dimethylacrylamide)
[(âĄ,N<sub>3</sub>)-PNIPAM<i>-<i>b</i>-</i>PDMA] and (âĄ,N<sub>3</sub>)-polystyrene<i>-<i>b</i>-</i>PNIPAM [(âĄ,N<sub>3</sub>)-PS<i>-<i>b</i>-</i>PNIPAM], with reactive alkyne and azide
at one end using a trifunctional agent enables us to study how their
self-assembly in a selective solvent affects interchain coupling,
i.e., the self-assembly assisted polypolymerization (SAAP). As expected,
(âĄ,N<sub>3</sub>)-PNIPAM<i>-<i>b</i>-</i>PDMA chains self-assemble into a micelle-like coreâshell structure
with a PNIPAM core in water at 50 °C. The coupling of as many
as 17 PNIAPM ends together led to star-like chains, independent of
the copolymer concentration, while the coupling efficiencies at lower
temperatures (with no self-assembly) and in good solvents are much
lower. These star-like chains remember their âbirthâ
state in water and undergo the intrachain contraction to form single-chain
micelles instead of large multichain aggregates. On the other hand,
(âĄ,N<sub>3</sub>)-PS<i>-<i>b</i>-</i>PNIPAM
exists as individual chains in THF, a mixture of unimers and micelles
in 2-propanol, the coreâshell micelles in methanol, and irregular
aggregates in water. Only in methanol, the coupling efficiency is
notably improved. The addition of water into 2-propanol enhances the
self-assembly and so does the interchain coupling. The current study
shows that even the solvophobic interaction makes the insoluble blocks
less mobile inside the core and decreases the collision probability
of reactive chain ends, the self-assembly still concentrates the reactive
ends together and assists the coupling if the selective solvent is
properly chosen
Comparative Study of Solution Properties of Amphiphilic 8âShaped Cyclic-(Polystyreneâ<i>b</i>âPoly(acrylic acid))<sub>2</sub> and Its Linear Precursor
Amphiphilic 8-shaped cyclic-(polystyrene-<i>b</i>-polyÂ(acrylic
acid))<sub>2</sub> with two rings and its linear precursor, i.e.,
8-shaped cyclic- and linear-(PSâPAA)<sub>2</sub>, were successfully
prepared by a combination of atom transfer radical polymerization
(ATRP) and âclickâ chemistry. Using various methods,
we characterized those intermediates and resultant copolymers and
studied their association properties in solutions. As expected, the
average aggregation number (âš<i>N</i><sub>agg</sub>â©) increases with the molar fraction of styrene for a given
overall degree of polymerization. Our results reveal that the cyclization
leads to a smaller âš<i>N</i><sub>agg</sub>â©
but slightly larger and looser aggregates, presumably due to the topological
constraint of the two rings (8-shaped). Using these amphiphilic chains
as emulsifying agents, we found that 8-shaped cyclic-(PSâPAA)<sub>2</sub> chains are less effective in stabilizing latex particles
in emulsion polymerization because each cyclic chain occupies a smaller
interfacial surface area than its linear counterpart. Further, using
pyrene as a model hydrophobic molecule, we investigated their solubilization
powers. Our results reveal that 8-shaped cyclic- and linear-(PSâPAA)<sub>2</sub> chains have a similar ability in loading hydrophobic pyrene
molecules, different from our original expectation, presumably because
the hydrophobic PS block is too short and the hydrophilic PAA rings
are too small. The current study provides a better understanding of
the complicated topological constraint on the solution properties
of 8-shaped cyclic amphiphilic copolymers
Construction and Properties of Hyperbranched Block Copolymer with Independently Adjustable Heterosubchains
A trifunctional initiator with one
alkyne, one hydroxyl, and one bromine group was used to construct
Br-polystyrene-alkyne-polyÂ(Δ-caprolactone)-OH (BrâPSââĄâPCLâOH) diblock copolymer
precursor with one terminal alkyne group located at the junction between the two
blocks. Further bromination and azidation substitution of the precursor led to a seesaw-type macromonomer azide-polystyrene-alkyne-poly(Δ-caprolactone)-azide (N<sub>3</sub>âPSââĄâPCLâN<sub>3</sub>). Subsequently,
novel hyperbranched copolymers [HB-(PS-<i>b</i>-PCL)<sub><i>n</i></sub>] with independently adjustable PS and PCL
branching subchains were prepared by âclickâ chemistry.
All of the linear precursors and hyperbranched copolymers were characterized
by FT-IR, <sup>1</sup>H NMR, and GPC with triple detectors in detail.
It was found that such hyperbranched copolymers are self-similar objects;
namely, their intrinsic viscosities ([η]) are scaled to the
weight-average molar masses (<i>M</i><sub>w</sub>) as [η]
⌠<i>M</i><sub>w</sub><sup>Μ</sup>, where Μ
= 0.45 ± 0.01 and 0.48 ± 0.01 for the longer and shorter
PS block, respectively. Moreover, the study on the crystallization
behavior of unfractionated and fractionated HB-(PS-<i>b</i>-PCL)<sub><i>n</i></sub> copolymers indicated both the
crystal size and the degree of crystallinity decrease with the PS
subchain length and the overall degree of polymerization, and the
remaining oligomer and macromonomer components could facilitate the
crystallization of the unfractionated sample. Finally, it was found
that the degree of crystallinity decreases dramatically when the weight
fraction of fractionated hyperbranched copolymer in macromonomer/hyperbranched
copolymer blend films exceeds âŒ67%, indicating that the uncrystallizable
hyperbranched chains may impose some extra restriction on the crystallization
of the macromonomer chains
DonorâAcceptor Porous Conjugated Polymers for Photocatalytic Hydrogen Production: The Importance of Acceptor Comonomer
Porous conjugated
polymer (PCP) is a new kind of photocatalyst
for photocatalytic hydrogen production (PHP). Here, we report the
importance of the electronic properties of acceptor comonomer in determining
the reactivity of 4,8-diÂ(thiophen-2-yl)ÂbenzoÂ[1,2-<i>b</i>:4,5-<i>b</i>âČ]Âdithiophene (DBD)-based PCP photocatalyst
for PHP application. It was found that the incorporation of nitrogen-containing
ligand acceptor monomers into PCP network is an effective strategy
to enhance the PHP activity. These moderately electron-deficient comonomers
enhanced the dipole polarization effect. These PCPs exhibit appropriate
solid-state morphology for charge transport. Powder X-ray diffraction
(XRD) studies demonstrate that these PCP materials are semicrystalline
materials. A strong correlation between the crystalline property and
PHP activity is observed. The replacement of nitrogen-containing ligand
acceptors with ligand-free strong acceptors is proved to be detrimental
to the PHP process, indicating the proper choice in the electronic
properties of monomer pair is important for achieving high photoactivity
Molecular Rectification Tuned by Through-Space Gating Effect
Inspired
by transistors and electron transfer in proteins, we designed a group
of pyridinoparacyclophane based diodes to study the through-space
electronic gating effect on molecular rectification. It was shown
that an edge-on gate effectively tunes the rectification ratio of
a diode via through-space interaction. Higher rectification ratio
was obtained for more electron-rich gating groups. The transition
voltage spectroscopy showed that the forward transition voltage is
correlated to the Hammett parameter of the gating group. Combining
theoretical calculation and experimental data, we proposed that the
change in rectification was induced by a shift in HOMO level both
spatially and energetically. This design principle based on through-space
edge-on gate is demonstrated on molecular wires, switches, and now
diodes, showing the potential of molecular design in increasing the
complexity of single-molecule electronic devices
Edge-on Gating Effect in Molecular Wires
This
work demonstrates edge-on chemical gating effect in molecular wires
utilizing the pyridinoparacyclophane (PC) moiety as the gate. Different
substituents with varied electronic demands are attached to the gate
to simulate the effect of varying gating voltages similar to that
in field-effect transistor (FET). It was observed that the orbital
energy level and charge carrierâs tunneling barriers can be
tuned by changing the gating group from strong electron acceptors
to strong electron donors. The single molecule conductance and currentâvoltage
characteristics of this molecular system are truly similar to those
expected for an actual single molecular transistor