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 “area” 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 = 0–3), intra-PDO (pair-wise diversity overlap) profile (g-q), and intra-MAD (maximal accrual diversity) profile (D_max-q) for the within-body biogeography of the human microbiome. These profiles constitute the “maps” 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 “average Joe” 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 “long tail” 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 = 0–3), intra-PDO (pair-wise diversity overlap) profile (g-q), and intra-MAD (maximal accrual diversity) profile (D_max-q) for the within-body biogeography of the human microbiome. These profiles constitute the “maps” 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 “average Joe” 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 “long tail” 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

Linear‑, Cyclic‑, and Multiblock Amphiphilic Polyelectrolytes as Surfactants in Emulsion Polymerization: Role of Topological Structure

Combining atom transfer radical polymerization (ATRP) and “click” chemistry, a set of well-defined amphiphilic block copolymers poly­(<i>n</i>-butyl acrylate)-<i>b</i>-poly­(acrylic acid) (P<i>n</i>BA₂₀-PAA₈₅) 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 ¹H 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>_p) and the concentration of polymeric surfactant with different topologies (<i>C</i>), i.e., <i>N</i>_p = <i>kC</i>^α, and the order of our measured exponent α is as follows: α_multi(1.10) > α_linear(0.81) ≥ α_cyclic(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>_p,multi > <i>N</i>_p,linear ≥ <i>N</i>_p,cyclic at higher concentration, and <i>N</i>_p,linear > <i>N</i>_p,cyclic ≥ <i>N</i>_p,multi at lower concentration was observed. Similar results (α_multi(1.02) > α_linear(0.65) ≥ α_cyclic(0.58)) were also observed when polystyrene-<i>b</i>-poly­(acrylic acid) (PS₉–PAA₆₀) 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, (≡,N₃)-poly­(<i>N</i>-isopropylacrylamide)-<i>b</i>-poly­(<i>N</i>,<i>N</i>-dimethylacrylamide) [(≡,N₃)-PNIPAM<i>-<i>b</i>-</i>PDMA] and (≡,N₃)-polystyrene<i>-<i>b</i>-</i>PNIPAM [(≡,N₃)-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, (≡,N₃)-PNIPAM<i>-<i>b</i>-</i>PDMA chains self-assemble into a micelle-like core–shell 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 “birth” state in water and undergo the intrachain contraction to form single-chain micelles instead of large multichain aggregates. On the other hand, (≡,N₃)-PS<i>-<i>b</i>-</i>PNIPAM exists as individual chains in THF, a mixture of unimers and micelles in 2-propanol, the core–shell 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 8‑Shaped Cyclic-(Polystyrene‑<i>b</i>‑Poly(acrylic acid))₂ and Its Linear Precursor

Amphiphilic 8-shaped cyclic-(polystyrene-<i>b</i>-poly­(acrylic acid))₂ with two rings and its linear precursor, i.e., 8-shaped cyclic- and linear-(PS–PAA)₂, were successfully prepared by a combination of atom transfer radical polymerization (ATRP) and “click” chemistry. Using various methods, we characterized those intermediates and resultant copolymers and studied their association properties in solutions. As expected, the average aggregation number (⟨<i>N</i>_agg⟩) increases with the molar fraction of styrene for a given overall degree of polymerization. Our results reveal that the cyclization leads to a smaller ⟨<i>N</i>_agg⟩ 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-(PS–PAA)₂ 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-(PS–PAA)₂ 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-poly­(ε-caprolactone)-OH (Br–PS–≡–PCL–OH) 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(ε-caprolactone)-azide (N₃–PS–≡–PCL–N₃). Subsequently, novel hyperbranched copolymers [HB-(PS-<i>b</i>-PCL)_<i>n</i>] with independently adjustable PS and PCL branching subchains were prepared by “click” chemistry. All of the linear precursors and hyperbranched copolymers were characterized by FT-IR, ¹H 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>_w) as [η] ∼ <i>M</i>_w^ν, where ν = 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)_<i>n</i> 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 ∼67%, indicating that the uncrystallizable hyperbranched chains may impose some extra restriction on the crystallization of the macromonomer chains

Donor–Acceptor 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-di­(thiophen-2-yl)­benzo­[1,2-<i>b</i>:4,5-<i>b</i>′]­dithiophene (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 carrier’s tunneling barriers can be tuned by changing the gating group from strong electron acceptors to strong electron donors. The single molecule conductance and current–voltage characteristics of this molecular system are truly similar to those expected for an actual single molecular transistor