In-situ measurements of the optical absorption of dioxythiophene-based conjugated polymers

Conjugated polymers can be reversibly doped by electrochemical means. This doping introduces new sub-bandgap optical absorption bands in the polymer while decreasing the bandgap absorption. To study this behavior, we have prepared an electrochemical cell allowing measurements of the optical properties of the polymer. The cell consists of a thin polymer film deposited on gold-coated Mylar behind which is another polymer that serves as a counterelectrode. An infrared transparent window protects the upper polymer from ambient air. By adding a gel electrolyte and making electrical connections to the polymer-on-gold films, one may study electrochromism in a wide spectral range. As the cell voltage (the potential difference between the two electrodes) changes, the doping level of the conjugated polymer films is changed reversibly. Our experiments address electrochromism in poly(3,4-ethylene-dioxy-thiophene) (PEDOT) and poly(3,4-dimethyl-propylene-dioxy-thiophene) (PProDOT-Me$_2$). This closed electrochemical cell allows the study of the doping induced sub-bandgap features (polaronic and bipolaronic modes) in these easily oxidized and highly redox switchable polymers. We also study the changes in cell spectra as a function of polymer thickness and investigate strategies to obtain cleaner spectra, minimizing the contributions of water and gel electrolyte features

Piliation of Invasive Streptococcus pneumoniae Isolates in the Era before Pneumococcal Conjugate Vaccine Introduction in Malawi

The pneumococcal pilus has been shown to be an important determinant of adhesion and virulence in mouse models of colonization, pneumonia, and bacteremia. A pilus is capable of inducing protective immunity, supporting its inclusion in next-generation pneumococcal protein vaccine formulations. Whether this vaccine target is common among pneumococci in sub-Saharan Africa is uncertain. To define the prevalence and genetic diversity of type I and II pili among invasive pneumococci in Malawi prior to the introduction of the 13-valent pneumococcal conjugate vaccine (PCV13) into routine childhood immunization, we examined 188 Streptococcus pneumoniae isolates collected between 2002 and 2008 (17% serotype 1). In this region of high disease burden, we found a low frequency of invasive piliated pneumococci (14%) and pilus gene sequence diversity similar to that seen previously in multiple global pneumococcal lineages. All common serotypes with pilus were covered by PCV13 and so we predict that pilus prevalence will be reduced in the Malawian pneumococcal population after PCV13 introduction

Genomic identification of a novel co-trimoxazole resistance genotype and its prevalence amongst Streptococcus pneumoniae in Malawi

Objectives This study aimed to define the molecular basis of co-trimoxazole resistance in Malawian pneumococci under the dual selective pressure of widespread co-trimoxazole and sulfadoxine/pyrimethamine use. Methods We measured the trimethoprim and sulfamethoxazole MICs and analysed folA and folP nucleotide and translated amino acid sequences for 143 pneumococci isolated from carriage and invasive disease in Malawi (2002–08). Results Pneumococci were highly resistant to both trimethoprim and sulfamethoxazole (96%, 137/143). Sulfamethoxazole-resistant isolates showed a 3 or 6 bp insertion in the sulphonamide-binding site of folP. The trimethoprim-resistant isolates fell into three genotypic groups based on dihydrofolate reductase (encoded by folA) mutations: Ile-100-Leu (10%), the Ile-100-Leu substitution together with a residue 92 substitution (56%) and those with a novel uncharacterized resistance genotype (34%). The nucleotide sequence divergence and dN/dS of folA and folP remained stable from 2004 onwards. Conclusions S. pneumoniae exhibit almost universal co-trimoxazole resistance in vitro and in silico that we believe is driven by extensive co-trimoxazole and sulfadoxine/pyrimethamine use. More than one-third of pneumococci employ a novel mechanism of co-trimoxazole resistance. Resistance has now reached a point of stabilizing evolution. The use of co-trimoxazole to prevent pneumococcal infection in HIV/AIDS patients in sub-Saharan Africa should be re-evaluated

Recombination in Streptococcus pneumoniae Lineages Increase with Carriage Duration and Size of the Polysaccharide Capsule.

Streptococcus pneumoniae causes a high burden of invasive pneumococcal disease (IPD) globally, especially in children from resource-poor settings. Like many bacteria, the pneumococcus can import DNA from other strains or even species by transformation and homologous recombination, which has allowed the pneumococcus to evade clinical interventions such as antibiotics and pneumococcal conjugate vaccines (PCVs). Pneumococci are enclosed in a complex polysaccharide capsule that determines the serotype; the capsule varies in size and is associated with properties including carriage prevalence and virulence. We determined and quantified the association between capsule and recombination events using genomic data from a diverse collection of serotypes sampled in Malawi. We determined both the amount of variation introduced by recombination relative to mutation (the relative rate) and how many individual recombination events occur per isolate (the frequency). Using univariate analyses, we found an association between both recombination measures and multiple factors associated with the capsule, including duration and prevalence of carriage. Because many capsular factors are correlated, we used multivariate analysis to correct for collinearity. Capsule size and carriage duration remained positively associated with recombination, although with a reduced P value, and this effect may be mediated through some unassayed additional property associated with larger capsules. This work describes an important impact of serotype on recombination that has been previously overlooked. While the details of how this effect is achieved remain to be determined, it may have important consequences for the serotype-specific response to vaccines and other interventions. IMPORTANCE: The capsule determines >90 different pneumococcal serotypes, which vary in capsule size, virulence, duration, and prevalence of carriage. Current serotype-specific vaccines elicit anticapsule antibodies. Pneumococcus can take up exogenous DNA by transformation and insert it into its chromosome by homologous recombination. This mechanism has disseminated drug resistance and generated vaccine escape variants. It is hence crucial to pneumococcal evolutionary response to interventions, but there has been no systematic study quantifying whether serotypes vary in recombination and whether this is associated with serotype-specific properties such as capsule size or carriage duration. Larger capsules could physically inhibit DNA uptake, or given the longer carriage duration for larger capsules, this may promote recombination. We find that recombination varies among capsules and is associated with capsule size, carriage duration, and carriage prevalence and negatively associated with invasiveness. The consequence of this work is that serotypes with different capsules may respond differently to selective pressures like vaccines

Diversity and inclusion in conservation: A proposal for a marine diversity network

Low diversity among scientists and practitioners is rampant in conservation. Currently, conservation professionals do not reflect the same diversity of perspectives and experiences of the world as the communities who bear the largest burden for implementing—or adverse consequences for failing to implement—conservation action. Acknowledging and describing the problem is important. But policies and programmes must also be put in place to correct it. Here, we highlight some measurable benefits of workforce diversity, and give an overview of some of the barriers to inclusion in marine conservation that help perpetuate low workforce diversity. Importantly, we underscore actions that both individuals and groups can take to alleviate such barriers. In particular, we describe the establishment of an online Marine Diversity Network, which conference participants proposed during a focus group meeting at the 4th International Marine Conservation Congress. The network will serve to bring together people from across the globe, from a variety of backgrounds, and from all career stages, to share knowledge, experiences and ideas, to provide and receive mentorship in marine conservation, and to forge new collaborations. Removing barriers to diverse participation requires coordinated, mindful actions by individuals and organizations. We hope that the proposed network and other actions presented in this paper find widespread support, and that they might serve both as inspiration and guide to other groups concerned with increasing diversity and inclusivity

Lachnospira pectinoschiza sp. nov., an Anaerobic Pectinophile from the Pig Intestine

Pectinophiles are bacteria that utilize pectin and only a few related compounds as substrates. Obligately anaerobic pectinophiles have been isolated from the intestinal tracts and gingivae of humans and from the rumina of cattle. We isolated three strains of pectinophilic bacteria from colonic contents of pigs but were unable to isolate pectinophiles from the rumen contents of four sheep, even when the animals were fed a high-pectin diet. The pectinophiles isolated from pigs were strictly anaerobic, motile, gram-positive rods (0.36 to 0.56 by 2.4 to 3.1 μm). Pectin, polygalacturonic acid, and gluconate were the only substrates that supported rapid growth. All three strains grew slowly on either lactose or cellobiose and fermented fructose after a lag of several days. Pectin was degraded by means of an extracellular pectin methylesterase and a Ca2+-dependent exopectate lyase. A comparison of the 16S rRNA sequences of these isolates with the 16S rRNA sequences of other gram-positive bacteria revealed a specific relationship with Lachnospira multipara (level of similarity, 94%). The Gram reaction, formation of spore-like structures, and the utilization of lactose and cellobiose differentiated the pig isolates from previously described pectinophiles. The pig isolates represent a previously undescribed species of the genus Lachnospira, for which we propose the name Lachnospira pectinoschiza

Scheduling language and algorithm development study. Volume 3: Detailed functional specifications for the language and module library

The detailed functional specifications presented are written as requirements for software implementation of the language and the program modules, and are aimed at a specific audience