Evaluation of a Culturally Responsive Mentorship Education Program for the Advisers of Howard Hughes Medical Institute Gilliam Program Graduate Students.

Effective mentorship is critical to the success of trainees in research career pathways, significantly impacting their research productivity, academic and research self-efficacy, and career satisfaction. Research faculty may be unaware of or unprepared to address mentor-mentee dynamics in mentoring relationships, especially those that go beyond traditional scientific skill development. Addressing mentorship dynamics can be even more challenging for mentors from well-represented backgrounds working with mentees from historically excluded racial/ethnic groups.

Teaching Undergraduates to Communicate Science, Cultivate Mentoring Relationships, and Navigate Science Culture.

The historic underrepresentation of women, certain racial and ethnic minorities, and members of other marginalized groups in careers in science, technology, engineering, and mathematics (STEM) reflects a disproportionate exit of individuals from these academic and career paths due to both environmental and personal factors. To transition successfully from classroom-based learning to the research environment, students must acquire various forms of capital nested within a largely hidden curriculum that most scientists learn informally. We have developed a semester-long course for undergraduate researchers that makes explicit concepts and strategies that contribute to STEM persistence.

Reassess-Realign-Reimagine: A Guide for Mentors Pivoting to Remote Research Mentoring.

Maintaining your research team's productivity during the COVID-19 era can be a challenge. Developing new strategies to mentor your research trainees in remote work environments will not only support research productivity and progress toward degree, but also help to keep your mentees' academic and research careers on track. We describe a three-step process grounded in reflective practice that research mentors and mentees can use together to , , and their mentoring relationships to enhance their effectiveness, both in the current circumstances and for the future.

Extensive global movement of multidrug-resistant strains revealed by whole-genome analysis.

Background: While the international spread of multidrug-resistant (MDR) strains is an acknowledged public health threat, a broad and more comprehensive examination of the global spread of MDR-tuberculosis (TB) using whole-genome sequencing has not yet been performed.

Methods: In a global dataset of 5310 . whole-genome sequences isolated from five continents, we performed a phylogenetic analysis to identify and characterise clades of MDR-TB with respect to geographic dispersion.

Probing sexual commitment at the single-cell level.

Malaria parasites go through major transitions during their complex life cycle, yet the underlying differentiation pathways remain obscure. Here we apply single cell transcriptomics to unravel the program inducing sexual differentiation in . Parasites have to make this essential life-cycle decision in preparation for human-to-mosquito transmission.

Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea.

We present two standards developed by the Genomic Standards Consortium (GSC) for reporting bacterial and archaeal genome sequences. Both are extensions of the Minimum Information about Any (x) Sequence (MIxS). The standards are the Minimum Information about a Single Amplified Genome (MISAG) and the Minimum Information about a Metagenome-Assembled Genome (MIMAG), including, but not limited to, assembly quality, and estimates of genome completeness and contamination.

Longitudinal genomic surveillance of Plasmodium falciparum malaria parasites reveals complex genomic architecture of emerging artemisinin resistance.

Background: Artemisinin-based combination therapies are the first line of treatment for Plasmodium falciparum infections worldwide, but artemisinin resistance has risen rapidly in Southeast Asia over the past decade. Mutations in the kelch13 gene have been implicated in this resistance. We used longitudinal genomic surveillance to detect signals in kelch13 and other loci that contribute to artemisinin or partner drug resistance.

Genomic analysis of globally diverse Mycobacterium tuberculosis strains provides insights into the emergence and spread of multidrug resistance.

Multidrug-resistant tuberculosis (MDR-TB), caused by drug-resistant strains of Mycobacterium tuberculosis, is an increasingly serious problem worldwide. Here we examined a data set of whole-genome sequences from 5,310 M. tuberculosis isolates from five continents.

Whole-Genome Sequencing of Mycobacterium tuberculosis Provides Insight into the Evolution and Genetic Composition of Drug-Resistant Tuberculosis in Belarus.

The emergence and spread of drug-resistant Mycobacterium tuberculosis (DR-TB) are critical global health issues. Eastern Europe has some of the highest incidences of DR-TB, particularly multidrug-resistant (MDR) and extensively drug-resistant (XDR) TB. To better understand the genetic composition and evolution of MDR- and XDR-TB in the region, we sequenced and analyzed the genomes of 138 M.

Structure of the germline genome of and relationship to the massively rearranged somatic genome.

The germline genome of the binucleated ciliate undergoes programmed chromosome breakage and massive DNA elimination to generate the somatic genome. Here, we present a complete sequence assembly of the germline genome and analyze multiple features of its structure and its relationship to the somatic genome, shedding light on the mechanisms of genome rearrangement as well as the evolutionary history of this remarkable germline/soma differentiation. Our results strengthen the notion that a complex, dynamic, and ongoing interplay between mobile DNA elements and the host genome have shaped chromosome structure, locally and globally.

Mobile genes in the human microbiome are structured from global to individual scales.

Recent work has underscored the importance of the microbiome in human health, and has largely attributed differences in phenotype to differences in the species present among individuals. However, mobile genes can confer profoundly different phenotypes on different strains of the same species. Little is known about the function and distribution of mobile genes in the human microbiome, and in particular whether the gene pool is globally homogenous or constrained by human population structure.

Population genomics studies identify signatures of global dispersal and drug resistance in Plasmodium vivax.

Plasmodium vivax is a major public health burden, responsible for the majority of malaria infections outside Africa. We explored the impact of demographic history and selective pressures on the P. vivax genome by sequencing 182 clinical isolates sampled from 11 countries across the globe, using hybrid selection to overcome human DNA contamination.

Genomic and functional analyses of Mycobacterium tuberculosis strains implicate ald in D-cycloserine resistance.

A more complete understanding of the genetic basis of drug resistance in Mycobacterium tuberculosis is critical for prompt diagnosis and optimal treatment, particularly for toxic second-line drugs such as D-cycloserine. Here we used the whole-genome sequences from 498 strains of M. tuberculosis to identify new resistance-conferring genotypes.

Draft Genome Sequences of Two Extensively Drug-Resistant Strains of Mycobacterium tuberculosis Belonging to the Euro-American S Lineage.

We report the whole-genome sequencing of two extensively drug-resistant tuberculosis strains belonging to the Euro-American S lineage. The RSA 114 strain showed single-nucleotide polymorphisms predicted to have drug efflux activity.

Populations of latent Mycobacterium tuberculosis lack a cell wall: Isolation, visualization, and whole-genome characterization.

Objective/background: Mycobacterium tuberculosis (MTB) causes active tuberculosis (TB) in only a small percentage of infected people. In most cases, the infection is clinically latent, where bacilli can persist in human hosts for years without causing disease. Surprisingly, the biology of such persister cells is largely unknown.

Genome analysis of three Pneumocystis species reveals adaptation mechanisms to life exclusively in mammalian hosts.

Pneumocystis jirovecii is a major cause of life-threatening pneumonia in immunosuppressed patients including transplant recipients and those with HIV/AIDS, yet surprisingly little is known about the biology of this fungal pathogen. Here we report near complete genome assemblies for three Pneumocystis species that infect humans, rats and mice. Pneumocystis genomes are highly compact relative to other fungi, with substantial reductions of ribosomal RNA genes, transporters, transcription factors and many metabolic pathways, but contain expansions of surface proteins, especially a unique and complex surface glycoprotein superfamily, as well as proteases and RNA processing proteins.

Sub-clinical detection of gut microbial biomarkers of obesity and type 2 diabetes.

Background: Obesity and type 2 diabetes (T2D) are linked both with host genetics and with environmental factors, including dysbioses of the gut microbiota. However, it is unclear whether these microbial changes precede disease onset. Twin cohorts present a unique genetically-controlled opportunity to study the relationships between lifestyle factors and the microbiome.