Multiple sequence alignment based on structural properties

A multiple sequence alignment (MSA) is a sequence alignment of three or more biological sequences. Main idea behind multiple sequence alignment is to see the similarities between input sequences, to be able to make phylogenetic analysis and other evolutionary conclusions. We propose a multiple sequence alignment method based on contact maps derived from structural data and network properties. We show that such methods may be useful in creating multiple alignments that can identify domains and similar structures where sequence identity is low

Growth Kinetics, Carbon Isotope Fractionation, and Gene Expression in the Hyperthermophile Methanocaldococcus jannaschii during Hydrogen-Limited Growth and Interspecies Hydrogen Transfer

Hyperthermophilic methanogens are often H2 limited in hot subseafloor environments, and their survival may be due in part to physiological adaptations to low H2 conditions and interspecies H2 transfer. The hyperthermophilic methanogen Methanocaldococcus jannaschii was grown in monoculture at high (80 to 83 μM) and low (15 to 27 μM) aqueous H2 concentrations and in coculture with the hyperthermophilic H2 producer Thermococcus paralvinellae. The purpose was to measure changes in growth and CH4 production kinetics, CH4 fractionation, and gene expression in M. jannaschii with changes in H2 flux. Growth and cell-specific CH4 production rates of M. jannaschii decreased with decreasing H2 availability and decreased further in coculture. However, cell yield (cells produced per mole of CH4 produced) increased 6-fold when M. jannaschii was grown in coculture rather than monoculture. Relative to high H2 concentrations, isotopic fractionation of CO2 to CH4(εCO2-CH4) was 16‰ larger for cultures grown at low H2 concentrations and 45‰ and 56‰ larger for M. jannaschii growth in coculture on maltose and formate, respectively. Gene expression analyses showed H2-dependent methylene-tetrahydromethanopterin (H4MPT) dehydrogenase expression decreased and coenzyme F420-dependent methylene-H4MPT dehydrogenase expression increased with decreasing H2 availability and in coculture growth. In coculture, gene expression decreased for membrane-bound ATP synthase and hydrogenase. The results suggest that H2 availability significantly affects the CH4 and biomass production and CH4 fractionation by hyperthermophilic methanogens in their native habitats

Ageism and sexuality

Sexuality remains important throughout a person’s life, but sexual behavior does not receive the same levels of acceptance at all ages. Older people are challenged by ageist attitudes and perceptions that hinder their sexual expression. They are stereotyped as non-sexual beings who should not, cannot, and do not want to have sexual relationships. Expressing sexuality or engaging in sexual activity in later life is considered by many in society as immoral or perverted. False expectations for older people also stem from ideals of beauty, centralization of the biomedical perspective on sexuality of older adults, and the association of sex with reproduction. Unfortunately, older people internalize many ageist attitudes towards sexuality in later life and become less interested in sex and less sexually active. The following chapter explores attitudes towards sexuality in later life among the media, young people, older people themselves, and care providers. In order to enable older people to express their sexuality and sexual identity freely and fully, awareness of ageist perceptions must be raised and defeated

The Metagenomics and Metadesign of the Subways and Urban Biomes (MetaSUB) International Consortium inaugural meeting report

The Metagenomics and Metadesign of the Subways and Urban Biomes (MetaSUB) International Consortium is a novel, interdisciplinary initiative comprised of experts across many fields, including genomics, data analysis, engineering, public health, and architecture. The ultimate goal of the MetaSUB Consortium is to improve city utilization and planning through the detection, measurement, and design of metagenomics within urban environments. Although continual measures occur for temperature, air pressure, weather, and human activity, including longitudinal, cross-kingdom ecosystem dynamics can alter and improve the design of cities. The MetaSUB Consortium is aiding these efforts by developing and testing metagenomic methods and standards, including optimized methods for sample collection, DNA/RNA isolation, taxa characterization, and data visualization. The data produced by the consortium can aid city planners, public health officials, and architectural designers. In addition, the study will continue to lead to the discovery of new species, global maps of antimicrobial resistance (AMR) markers, and novel biosynthetic gene clusters (BGCs). Finally, we note that engineered metagenomic ecosystems can help enable more responsive, safer, and quantified cities

Psychometric properties of the Alcohol Use Disorders Identification Test (AUDIT) across cross-cultural subgroups, genders, and sexual orientations: Findings from the International Sex Survey (ISS)

© 2023 The Authors. Published by Elsevier Inc. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/bync-nd/4.0/).INTRODUCTION: Despite being a widely used screening questionnaire, there is no consensus on the most appropriate measurement model for the Alcohol Use Disorders Identification Test (AUDIT). Furthermore, there have been limited studies on its measurement invariance across cross-cultural subgroups, genders, and sexual orientations. AIMS: The present study aimed to examine the fit of different measurement models for the AUDIT and its measurement invariance across a wide range of subgroups by country, language, gender, and sexual orientation. METHODS: Responses concerning past-year alcohol use from the participants of the cross-sectional International Sex Survey were considered (N = 62,943; M age: 32.73; SD = 12.59). Confirmatory factor analysis, as well as measurement invariance tests were performed for 21 countries, 14 languages, three genders, and four sexual-orientation subgroups that met the minimum sample size requirement for inclusion in these analyses. RESULTS: A two-factor model with factors describing 'alcohol use' (items 1-3) and 'alcohol problems' (items 4-10) showed the best model fit across countries, languages, genders, and sexual orientations. For the former two, scalar and latent mean levels of invariance were reached considering different criteria. For gender and sexual orientation, a latent mean level of invariance was reached. CONCLUSIONS: In line with the two-factor model, the calculation of separate alcohol-use and alcohol-problem scores is recommended when using the AUDIT. The high levels of measurement invariance achieved for the AUDIT support its use in cross-cultural research, capable also of meaningful comparisons among genders and sexual orientations.Peer reviewe

Problematic pornography use across countries, genders, and sexual orientations: Insights from the International Sex Survey and comparison of different assessment tools.

Problematic pornography use (PPU) is a common manifestation of the newly introduced Compulsive Sexual Behavior Disorder diagnosis in the 11th edition of the International Statistical Classification of Diseases and Related Health Problems. Although cultural, gender- and sexual orientation-related differences in sexual behaviors are well documented, there is a relative absence of data on PPU outside Western countries and among women as well as gender- and sexually-diverse individuals. We addressed these gaps by (a) validating the long and short versions of the Problematic Pornography Consumption Scale (PPCS and PPCS-6, respectively) and the Brief Pornography Screen (BPS) and (b) measuring PPU risk across diverse populations. Using data from the pre-registered International Sex Survey [n = 82 243; mean age (M <sub>age</sub> ) = 32.4 years, standard deviation = 12.5], a study across 42 countries from five continents, we evaluated the psychometric properties (i.e. factor structure, measurement invariance, and reliability) of the PPCS, PPCS-6, and BPS and examined their associations with relevant correlates (e.g. treatment-seeking). We also compared PPU risk among diverse groups (e.g. three genders). The PPCS, PPCS-6, and BPS demonstrated excellent psychometric properties [for example, comparative fit index = 0.985, Tucker-Lewis Index = 0.981, root mean square error of approximation = 0.060 (90% confidence interval = 0.059-0.060)] in the confirmatory factor analysis, with all PPCS' inter-factor correlations positive and strong (rs = 0.72-0.96). A total of 3.2% of participants were at risk of experiencing PPU (PPU+) based on the PPCS, with significant country- and gender-based differences (e.g. men reported the highest levels of PPU). No sexual orientation-based differences were observed. Only 4-10% of individuals in the PPU+ group had ever sought treatment for PPU, while an additional 21-37% wanted to, but did not do so for specific reasons (e.g. unaffordability). This study validated three measures to assess the severity of problematic pornography use across languages, countries, genders, and sexual orientations in 26 languages: the Problematic Pornography Consumption Scale (PPCS, and PPCS-6, respectively), and the Brief Pornography Screen (BPS). The problematic pornography use risk is estimated to be 3.2-16.6% of the population of 42 countries, and varies among different groups (e.g. genders) and based on the measure used