Customer Publications

Here’s the latest published research from our customers.

Our customers are doing some really great things. If you’re curious about what they’re up to and how we’re helping, check out the articles below.

the Marine Fish Species Genypterus chilensis and Seriolella violacea

Cultivable Yeast Microbiota from the Marine Fish Species Genypterus chilensis and Seriolella violacea

Gut microbiota can be a source of novel yeasts with the potential to be used as probiotics or have industrial applications. In this work, scientists characterized two as-of-yet unexplored yeast communities from the intestinal content of the cultured marine Chilean fishes Genypterus chilensis and Seriolella violacea.

B Valderrama, JJ Ruiz, MS Gutiérrez, K Alveal… – Journal of Fungi, 2021

Identification of novel and rare variants associated with handgrip strength using whole genome sequence data from the NHLBI Trans-Omics in Precision Medicine …

Previous genome-wide association studies of handgrip strength have focused on common variants primarily in persons of European descent. Scientists aimed to identify rare and ancestry-specific genetic variants associated with handgrip strength by conducting whole-genome sequence association analyses using 13,552 participants from six studies representing diverse population groups from the Trans-Omics in Precision Medicine (TOPMed) Program.

C Sarnowski, H Chen, ML Biggs… – PloS one, 2021

Oomycetes associated with Prunus serotina persist in soil after tree harvest

Scientists studied the presence of oomycetes and evaluated seedling performance in soils near live Prunus serotina trees, and 0.5 and 1.5 year old stumps. Five species of oomycetes were isolated from soils, two of which were pathogenic (Pythium intermedium and Pythium irregulare) to Prunus serotina. There was a non-significant ~10.5% increase in conspecific seedling survival in stumps versus live trees, and pathogens were present in soils of all stump ages.

CM Esch, CM Medina-Mora, RK Kobe, ML Sakalidis – Fungal Ecology, 2021

Airbrone

Agricultural practices drive biological loads, seasonal patterns and potential pathogens in the aerobiome of a mixed-land-use dryland

The aerobiome is known to contain microbes, including pathogens, as well as debris or small-sized propagules from plants and animals, but its variability and composition has not been studied comprehensibly. To gain a dynamic insight into the aerobiome existing over a mixed-use dryland setting, scientists conducted a biologically comprehensive, year-long survey of its composition and dynamics for particles less than 10 μm in diameter based on quantitative analyses of DNA content coupled to genomic sequencing.

DR Finn, J Maldonado, F de Martini, J Yu, CR Penton…

Complex evolutionary history of felid anelloviruses

Anellovirus infections are highly prevalent in mammals, however, prior to this study only a handful of anellovirus genomes had been identified in members of the Felidae family. Here scientists characterized anelloviruses in pumas (Puma concolor), bobcats (Lynx rufus), Canadian lynx (Lynx canadensis), caracals (Caracal caracal) and domestic cats (Felis catus). The complete anellovirus genomes (n = 220) recovered from 149 individuals were diverse.

S Kraberger, LEK Serieys, C Richet… – Virology, 2021

Mechanisms and consequences of casein kinase II and ankyrin-3 regulation of the epithelial Na+ channel

The CKII phosphorylation site in ENaC resides within a canonical “anchor” ankyrin binding motif. CKII-dependent phosphorylation of ENaC is necessary and sufficient to increase channel activity and is thought to influence channel trafficking in a manner that increases activity. Scientists tested the hypothesis that phosphorylation of ENaC by CKII within an anchor motif is necessary for ankyrin-3 (Ank-3) regulation of the channel, which is required for normal channel locale and function, and the proper regulation of renal sodium excretion.

TM Abd El-Aziz, AG Soares, E Mironova, N Boiko… – Scientific Reports, 2021

The HIF target MAFF promotes tumor invasion and metastasis through IL11 and STAT3 signaling

Hypoxia plays a critical role in tumor progression including invasion and metastasis. To determine critical genes regulated by hypoxia that promote invasion and metastasis, scientists screened 50 hypoxia inducible genes for their effects on invasion. Researchers identified v-maf musculoaponeurotic fibrosarcoma oncogene homolog F (MAFF) as a potent regulator of tumor invasion without affecting cell viability.

EJ Moon, SS Mello, CG Li, JT Chi, K Thakkar… – Nature Communications, 2021

Identification of a GrgA-Euo-HrcA Transcriptional Regulatory Network in Chlamydia

Chlamydia trachomatis is an obligate intracellular bacterium whose unique developmental cycle consists of an infectious elementary body and a replicative reticulate body. Progression of this developmental cycle requires temporal control of the transcriptome. In addition to the three chlamydial sigma factors (σ66, σ28, and σ54) that recognize promoter sequences of genes, chlamydial transcription factors are expected to play crucial roles in transcriptional regulation. Here, scientists investigated the function of GrgA, a Chlamydiaspecific transcription factor, in C. trachomatis transcriptomic expression.

W Wurihan, Y Zou, AM Weber, K Weldon, Y Huang… – mSystems, 2021

Allelic Diversity at Abiotic Stress Responsive Genes in Relationship to Ecological Drought Indices for Cultivated Tepary Bean, Phaseolus acutifolius A. Gray, and Its Wild Relatives

Some of the major impacts of climate change are expected in regions where drought stress is already an issue. Grain legumes are generally drought susceptible. However, tepary bean and its wild relatives within Phaseolus acutifolius are from arid areas between Mexico and the United States. Therefore, scientists hypothesized that these bean accessions have diversity signals indicative of adaptation to drought at key candidate genes such as: Asr2, Dreb2B, and ERECTA. By sequencing alleles of these genes and comparing to estimates of drought tolerance indices from climate data for the collection site of geo-referenced, tepary bean accessions, researchers determined the genotype x environmental association (GEA) of each gene.

Academic Editor: Cesar Arrese-Igor

Chromosome Xq23 is associated with lower atherogenic lipid concentrations and favorable cardiometabolic indices

Autosomal genetic analyses of blood lipids have yielded key insights for coronary heart disease (CHD). However, X chromosome genetic variation is understudied for blood lipids in large sample sizes. Scientists analyzed genetic and blood lipid data in a high-coverage whole X chromosome sequencing study of 65,322 multi-ancestry participants and performed replication among 456,893 European participants.

Generation of fourteen isogenic cell lines for Parkinson’s disease-associated leucine-rich repeat kinase (LRRK2)

Mutations in leucine-rich repeat kinase 2 (LRRK2) are associated with inherited forms of Parkinson’s disease (PD), causing disease by a gain of kinase function. Here, scientists describe a series of isogenic iPSC lines with any of five pathogenic mutations (N1437H, R1441C, Y1699C, G2019S and I2020T); two hypothesis testing mutations (GTP binding null, T1348N, and kinase dead, K1906M) and two LRRK2 knockouts. This resource could be used to assess effects of mutations on the function of endogenous LRRK2 and/or to study LRRK2 interactors and substrates in iPSC-derived cellular models.

Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20892, USA

GrgA overexpression inhibits Chlamydia trachomatis growth through sigma66– and sigma28-dependent mechanisms

This study aimed to biochemically characterize interactions between two Synechococcus elongatus proteins and cyclic-di- AMP and other potential nucleotide ligands. Both of these proteins, SeCR1 and SsbP, have been shown to interact with cyclic-di-AMP in a previous study, however neither had KD values reported.

a
Department of Pharmacology, Robert Wood Johnson Medical School, Rutgers The State University of New Jersey, Piscataway, NJ, 08854, USA
b
Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, 730046, China

Fusarium root rot complex in soybean: Molecular characterization, trichothecene formation and cross-pathogenicity.

Here, scientists investigated the Fusarium root rot complex in Manitoba (Canada) from symptomatic plants, using both culture- and molecular-based methods. Researchers developed a molecular diagnostic toolkit to detect and differentiate between several Fusarium spp. involved in FHB and FRR, followed by an evaluation of cross-pathogenicity of selected Fusarium isolates collected from soybean and wheat, and the results indicate that isolates recovered from one host can infect the other host.

Mohamed Hafez, Ahmed Abdelmagid,Reem Aboukhaddour, Lorne R. Adam, and Fouad Daayf 

Published Online: 

Structural basis of KdpD histidine kinase binding to the second messenger c-di-AMP

The KdpDE two-component system regulates potassium homeostasis and virulence in various bacterial species. The KdpD histidine kinases (HK) of this system contain a universal stress protein (USP) domain which binds to the second messenger cyclic-di-adenosine monophosphate (c-di-AMP) for regulating transcriptional output from this two-component system in Firmicutes such as Staphylococcus aureus. However, the structural basis of c-di-AMP specificity within the KdpD-USP domain is not well understood.

AnirudhaDutta, MonaBatish, VijayParashar

Identification of novel circovirus and anelloviruses from wolverines using a non-invasive faecal sampling approach

Little is known about viruses associated with wild wolverines. An investigation of the faecal samples resulted in the identification of a novel circovirus from three out of four wolverine samples, two collected in 2018 and one in 2019. Comparison with other circoviruses shows it is most closely related to a porcine circovirus 3, sharing ~69% identity.

Diverse immune response of DNA damage repair-deficient tumors

Scientists integrated deleterious somatic and germline mutations and methylation data of DDR genes in 10,080 cancers representing 32 cancer types and evaluated the associations of these alterations with tumor neoantigens and immune infiltrates. Analyses identified DDR pathway mutations that are associated with higher neoantigen loads, adaptive immune markers, and survival outcomes of immune checkpoint inhibitor-treated animal models and patients.

An approach to rapid characterization of DMD copy number variants for prenatal risk assessment

Scientists identified a duplication of uncertain significance encompassing a portion of the dystrophin gene (DMD) in an unaffected mother and her male fetus. Using long-read whole genome sequencing and alignment of short reads, researchers rapidly defined the precise breakpoints of this variant in DMD and could provide timely counseling. The benign nature of the variant was substantiated, more slowly, by familial segregation to a healthy maternal uncle.

A Chromosome-Level Genome Assembly of the Parasitoid Wasp, Cotesia glomerata (Hymenoptera: Braconidae)

Hymenopterans make up about 20% of all animal species, but most are poorly known and lack high-quality genomic resources. One group of important yet understudied hymenopterans are parasitoid wasps in the family Braconidae. Among this understudied group is the genus Cotesia, a clade of ~1,000 species routinely used in studies of physiology, ecology, biological control, and genetics. However, the ability to understand these organisms has been hindered by a lack of genomic resources. Scientists helped bridge this gap by generating a high-quality genome assembly for the parasitoid wasp, Cotesia glomerata (Braconidae; Microgastrinae).

Journal of Heredity, esab032

Lentinula madagasikarensis sp. nov., a relative of shiitake mushrooms from Madagascar

Scientists describe the first species of Lentinula from Africa, Lentinula madagasikarensis sp. nov. The new taxon, which was collected from central Madagascar, is strikingly similar to L. edodes, the shiitake mushroom. A BLAST search using ITS sequences from L. madagasikarensis as the query retrieves a mix of Lentinula, Gymnopus, Marasmiellus, and other members of Omphalotaceae as the top hits. A 28S phylogeny of the Omphalotaceae confirms placement of L.madagasikarensis within Lentinula.

B.P. Looney, B. Buyck, N. Menolli Jr., E. Randrianjohany, D. Hibbett1

Development of a novel Live Attenuated Influenza A Virus vaccine encoding the IgA-inducing protein.

Live attenuated influenza virus (LAIV) vaccines elicit a combination of systemic and mucosal immunity by mimicking a natural infection. To further enhance protective mucosal responses, scientists incorporated the gene encoding the IgA-inducing protein (IGIP) into the LAIV genomes of the cold-adapted A/Leningrad/134/17/57 (H2N2) strain (caLen) and the experimental attenuated backbone A/turkey/Ohio/313053/04 (H3N2) (OH/04att). Incorporation of IGIP into the caLen background led to a virus that grew poorly in prototypical substrates. In contrast, IGIP in the OH/04att background (IGIP-H1att) virus grew to titers comparable to the isogenic backbone H1att (H1N1) without IGIP. IGIP-H1att- and H1caLen-vaccinated mice were protected against lethal challenge with a homologous virus.

C. Joaquín Cáceres, Stivalis Cardenas-Garcia, Aarti Jain, L. Claire Gay, Silvia Carnaccini, Brittany Seibert, Lucas M. Ferreri1, Ginger Geiger1, Alguimantas Jasinskas2, Rie Nakajima2, Daniela S. Rajao1, Irina Isakova-Sivak, Larisa Rudenko4, Amy L. Vincent5, D. Huw Davies2 and Daniel R. Perez

Mutation E48K in PB1 Polymerase Subunit Improves Stability of a Candidate Live Attenuated Influenza B Virus Vaccine

Influenza B virus (IBV) is a major respiratory pathogen of humans, particularly in the elderly and children, and vaccines are the most effective way to control it. In previous work, incorporation of two mutations (E580G, S660A) along with the addition of an HA epitope tag in the PB1 segment of B/Brisbane/60/2008 (B/Bris) resulted in an attenuated strain that was safe and effective as a live attenuated vaccine.

SUBSCRIBE TO OUR MONTHLY NEWSLETTER

Please select the area(s) of research you are interested in.

Psomagen, Inc. needs the contact information you provide to us to contact you about our products and services. You may unsubscribe from these communications at any time. For information on how to unsubscribe, as well as our privacy practices and commitment to protecting your privacy, please review our Privacy Policy.

3 + 2 = ?