bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genome sequencing of 15 acid-tolerant yeasts
Authors: Bagley James A. , Pyne Michael E. , Exley Kealan , Kevvai Kaspar , Wang Qingzhao , Whiteway Malcolm , Martin Vincent J. J. 
Published: September 2023

ABSTRACT

We report draft genome sequences for 15 non-conventional Saccharomycotina yeast strains obtained from public culture repositories. Included in our collection are eight strains of
Pichia
with broad tolerance to dicarboxylic acids. The genome sequences of these strains will enable comparative genomics of acid-tolerant phenotypes and strain engineering of non-conventional hosts.
Complete genome sequence of
Candidatus
Mycobacterium wuenschmannii
,
a nontuberculous mycobacterium isolated from a captive population of Amazon milk frogs
Authors: Zeineldin Mohamed , Hicks Jessica , Ward Hilary J. , Wünschmann Arno , Camp Patrick , Farrell David , Lehman Kimberly , Thacker Tyler C. , Cuthbert Elizabeth 
Published: September 2023

ABSTRACT
A slow growing species of nontuberculous mycobacteria (NTM) was isolated from the liver of an Amazon milk frog. The complete genome of this isolate comprises 5,102,433 bp, exhibiting 66.86% GC content, 4,940 protein-coding sequences, 52 predicted RNA genes, and 39 repeat regions.
Whole-genome sequence of
Paenibacillus amylolyticus
strain W018, isolated from
Triticum aestivum
L. seeds, obtained using nanopore sequencing
Authors: Chebotar Vladimir K. , Gancheva Maria S. , Chizhevskaya Elena P. , Keleinikova Oksana V. , Baganova Maria E. , Zaplatkin Alexander N. , Husainov Kharon A. 
Published: September 2023

ABSTRACT

In this study, we performed nanopore sequencing of the genome of
Paenibacillus amylolyticus
strain W018, isolated from the seeds of winter wheat, cv. Bezostaya 100. The genome size is 7.07 Mb, with a GC content of 45.8%, and contains 8,190 genes.
Uracil-DNA glycosylase of murine gammaherpesvirus 68 binds cognate viral replication factors independently of its catalytic residues
Authors: Smith Kyle R. , Paul Somnath , Dong Qiwen , Anannya Orchi , Oldenburg Darby G. , Forrest J. Craig , McBride Kevin M. , Krug Laurie T. 
Published: September 2023

ABSTRACT

Herpesviruses are large double-stranded DNA viruses that encode core replication proteins and accessory factors involved in nucleotide metabolism and DNA repair. Mammalian uracil-DNA glycosylases (UNG) excise deleterious uracil residues from their genomic DNA. Each herpesvirus UNG studied to date has demonstrated conservation of the enzymatic function to excise uracil residues from DNA. We previously reported that a murine gammaherpesvirus (MHV68) with a stop codon in
ORF46
(ORF46.stop) that encodes for vUNG was defective in lytic replication and latency
in vivo
. However, a mutant virus that expressed a catalytically inactive vUNG (ORF46.CM) had no replication defect unless coupled with additional mutations in the catalytic motif of the viral dUTPase (ORF54.CM). The disparate phenotypes observed in the vUNG mutants led us to explore the non-enzymatic properties of vUNG. Immunoprecipitation of vUNG followed by mass spectrometry in MHV68-infected fibroblasts identified a complex comprising the cognate viral DNA polymerase, vPOL, encoded by
ORF9
, and the viral DNA polymerase processivity factor, vPPF, encoded by
ORF59
. MHV68 vUNG co-localized with vPOL and vPPF in subnuclear structures consistent with viral replication compartments. In reciprocal co-immunoprecipitations, the vUNG formed a complex with the vPOL and vPPF upon transfection with either factor alone or in combination. Lastly, we determined that key catalytic residues of vUNG are not required for interactions with vPOL and vPPF upon transfection or in the context of infection. We conclude that the vUNG of MHV68 associates with vPOL and vPPF independently of its catalytic activity.

IMPORTANCE

Gammaherpesviruses encode a uracil-DNA glycosylase (vUNG) that is presumed to excise uracil residues from viral genomes. We previously identified the vUNG enzymatic activity, but not the protein itself, as dispensable for gammaherpesvirus replication
in vivo
. In this study, we report a non-enzymatic role for the viral UNG of a murine gammaherpesvirus in forming a complex with two key components of the viral DNA replication machinery. Understanding the role of the vUNG in this viral DNA replication complex may inform the development of antiviral drugs that combat gammaherpesvirus-associated cancers.
Identification of the alternative sigma factor regulons of
Chlamydia trachomatis
using multiplexed CRISPR interference
Authors: Hatch Nathan D. , Ouellette Scot P. 
Published: September 2023

ABSTRACT

Chlamydia trachomatis
is a developmentally regulated, obligate intracellular bacterium that encodes three sigma factors: σ66, σ54, and σ28. σ66 is the major sigma factor controlling most transcription initiation during early- and mid-cycle development as the infectious elementary body (EB) transitions to the non-infectious reticulate body (RB) that replicates within an inclusion inside the cell. The roles of the minor sigma factors, σ54 and σ28, have not been well characterized to date; however, there are data to suggest each functions in late-stage development and secondary differentiation as RBs transition to EBs. As the process of secondary differentiation itself is poorly characterized, clarifying the function of these alternative sigma factors by identifying the genes regulated by them will further our understanding of chlamydial differentiation. We hypothesize that σ54 and σ28 have non-redundant and essential functions for initiating late gene transcription thus mediating secondary differentiation in
Chlamydia
. Here, we demonstrate the necessity of each minor sigma factor in successfully completing the developmental cycle. We have implemented and validated multiplexed Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) interference techniques, novel to the chlamydial field to examine the effects of knocking down each alternative sigma factor individually and simultaneously. In parallel, we also overexpressed each sigma factor. Altering transcript levels for either or both alternative sigma factors resulted in a severe defect in EB production as compared to controls. Furthermore, RNA sequencing identified differentially expressed genes during alternative sigma factor dysregulation, indicating the putative regulons of each. These data demonstrate that the levels of alternative sigma factors must be carefully regulated to facilitate chlamydial growth and differentiation.

IMPORTANCE

Chlamydia trachomatis
is a significant human pathogen in both developed and developing nations. Due to the organism's unique developmental cycle and intracellular niche, basic research has been slow and arduous. However, recent advances in chlamydial genetics have allowed the field to make significant progress in experimentally interrogating the basic physiology of
Chlamydia
. Broadly speaking, the driving factors of chlamydial development are poorly understood, particularly regarding how the later stages of development are regulated. Here, we employ a novel genetic tool for use in
Chlamydia
while investigating the effects of dysregulating the two alternative sigma factors in the organism that help control transcription initiation. We provide further evidence for both sigma factors' essential roles in late-stage development and their potential regulons, laying the foundation for deeper experimentation to uncover the molecular pathways involved in chlamydial differentiation.
Cell behaviors underlying
Myxococcus xanthus
aggregate dispersal
Authors: Murphy Patrick , Comstock Jessica , Khan Trosporsha , Zhang Jiangguo , Welch Roy , Igoshin Oleg A. 
Published: September 2023

ABSTRACT

The soil bacterium
Myxococcus xanthus
is a model organism with a set of diverse behaviors. These behaviors include the starvation-induced multicellular development program, in which cells move collectively to assemble multicellular aggregates. After initial aggregates have formed, some will disperse, with smaller aggregates having a higher chance of dispersal. Initial aggregation is driven by two changes in cell behavior: cells slow down inside of aggregates and bias their motion by reversing direction less frequently when moving toward aggregates. However, the cell behaviors that drive dispersal are unknown. Here, we use fluorescent microscopy to quantify changes in cell behavior after initial aggregates have formed. We observe that after initial aggregate formation, cells adjust the bias in reversal timings by initiating reversals more rapidly when approaching unstable aggregates. Using agent-based modeling, we then show dispersal is predominantly generated by this change in bias, which is strong enough to overcome slowdown inside aggregates. Notably, the change in reversal bias is correlated with the nearest aggregate size, connecting cellular activity to previously observed correlations between aggregate size and fate. To determine if this connection is consistent across strains, we analyze a second
M. xanthus
strain with reduced levels of dispersal. We find that far fewer cells near smaller aggregates modified their bias. This implies that aggregate dispersal is under genetic control, providing a foundation for further investigations into the role it plays in the life cycle of
M. xanthus
.

Importance

Understanding the processes behind bacterial biofilm formation, maintenance, and dispersal is essential for addressing their effects on health and ecology. Within these multicellular communities, various cues can trigger differentiation into distinct cell types, allowing cells to adapt to their specific local environment. The soil bacterium
Myxococcus xanthus
forms biofilms in response to starvation, marked by cells aggregating into mounds. Some aggregates persist as spore-filled fruiting bodies, while others disperse after initial formation for unknown reasons. Here, we use a combination of cell tracking analysis and computational simulations to identify behaviors at the cellular level that contribute to aggregate dispersal. Our results suggest that cells in aggregates actively determine whether to disperse or persist and undergo a transition to sporulation based on a self-produced cue related to the aggregate size. Identifying these cues is an important step in understanding and potentially manipulating bacterial cell-fate decisions.
Oxygen evolution from extremophilic cyanobacteria confined in hard biocoatings
Authors: Krings Simone , Chen Yuxiu , Keddie Joseph L. , Hingley-Wilson Suzanne 
Published: September 2023

ABSTRACT

Biocoatings, in which viable bacteria are immobilized within a waterborne polymer coating for a wide range of potential applications, have garnered greater interest in recent years. In bioreactors, biocoatings can be ready-to-use alternatives for carbon capture or biofuel production that could be reused multiple times. Here, we have immobilized cyanobacteria in mechanically hard biocoatings, which were deposited from polymer colloids in water (i.e
.,
latex). The biocoatings are formed upon heating to 37°C and fully dried before rehydrating. The viability and oxygen evolution of three cyanobacterial species within the biocoatings were compared.
Synechococcus
sp. PCC 7002 was non-viable inside the biocoatings immediately after drying, whereas
Synechocystis
sp. PCC 6803 survived the coating formation, as shown by an adenosine triphosphate (ATP) assay.
Synechocystis
sp. PCC 6803 consumed oxygen (by cell respiration) for up to 5 days, but was unable to perform photosynthesis, as indicated by a lack of oxygen evolution. However,
Chroococcidiopsis cubana
PCC 7433, a strain of desiccation-resistant extremophilic cyanobacteria, survived and performed photosynthesis and carbon capture within the biocoating, with specific rates of oxygen evolution up to 0.4 g of oxygen/g of biomass per day. Continuous measurements of dissolved oxygen were carried out over a month and showed no sign of decreasing activity. Extremophilic cyanobacteria are viable in a variety of environments, making them ideal candidates for use in biocoatings and other biotechnology.

IMPORTANCE

As water has become a precious resource, there is a growing need for less water-intensive use of microorganisms, while avoiding desiccation stress. Mechanically robust, ready-to-use biocoatings or “living paints” (a type of artificial biofilm consisting of a synthetic matrix containing functional bacteria) represent a novel way to address these issues. Here, we describe the revolutionary, first-ever use of an extremophilic cyanobacterium (
Chroococcidiopsis cubana
PCC 7433) in biocoatings, which were able to produce high levels of oxygen and carbon capture for at least 1 month despite complete desiccation and subsequent rehydration. Beyond culturing viable bacteria with reduced water resources, this pioneering use of extremophiles in biocoatings could be further developed for a variety of applications, including carbon capture, wastewater treatment and biofuel production.
Impacts of biostimulation and bioaugmentation on woodchip bioreactor microbiomes
Authors: Wang Hao , Feyereisen Gary W. , Wang Ping , Rosen Carl , Sadowsky Michael J. , Ishii Satoshi 
Published: September 2023

ABSTRACT

Woodchip bioreactors (WBRs) are used to remove nutrients, especially nitrate, from subsurface drainage. The nitrogen removal efficiency of WBRs, however, is limited by low temperatures and the availability of labile carbon. Bioaugmentation and biostimulation are potential approaches to enhance nitrate removal of WBRs under cold conditions, but their effectiveness is still unclear. Here, we clarified the effects of bioaugmentation and biostimulation on the microbiomes and nitrate removal rates of WBRs. As a bioaugmentation treatment, we inoculated WBR-borne cold-adapted denitrifying bacteria
Cellulomonas cellasea
strain WB94 and
Microvirgula aerodenitrificans
strain BE2.4 into the WBRs located at Willmar, MN, USA. As a biostimulation treatment, acetate was added to the WBRs to promote denitrification. Woodchip samples were collected from multiple locations in each WBR before and after the treatments and used for the microbiome analysis. The 16S rRNA gene amplicon sequencing showed that the microbiomes changed by the treatments and season. The high-throughput quantitative PCR for nitrogen cycle genes revealed a higher abundance of denitrification genes at locations closer to the WBR inlet, suggesting that denitrifiers are unevenly present in WBRs. In addition, a positive relationship was identified between the abundance of
M. aerodenitrificans
strain BE2.4 and those of
norB
and
nosZ
in the WBRs. Based on generalized linear modeling, the abundance of
norB
and
nosZ
was shown to be useful in predicting the nitrate removal rate of WBRs. Taken together, these results suggest that the bioaugmentation and biostimulation treatments can influence denitrifier populations, thereby influencing the nitrate removal of WBRs.

IMPORTANCE
Nitrate pollution is a serious problem in agricultural areas in the U.S. Midwest and other parts of the world. Woodchip bioreactor is a promising technology that uses microbial denitrification to remove nitrate from agricultural subsurface drainage, although the reactor’s nitrate removal performance is limited under cold conditions. This study showed that the inoculation of cold-adapted denitrifiers (i.e., bioaugmentation) and the addition of labile carbon (i.e., biostimulation) can influence the microbial populations and enhance the reactor’s performance under cold conditions. This finding will help establish a strategy to mitigate nitrate pollution.
Prognostic Value of Neutrophil-to-Lymphocyte Ratio and Vaccination for Negative Conversion Time of Nucleic Acid in Nonsevere COVID-19 Patients Infected by SARS-CoV-2 Omicron Variant
Authors: Zhu Kongbo , Ma Shaolei , Chen Hui , Xie Jianfeng , Huang Dan , Hou Zhenghua , Qiu Shanhu , Ma Genshan , Huang Yingzi 
Published: September 2023

SARS-CoV-2 Omicron variant is significantly different from all the previous variants and has rapidly replaced other variants as the dominant variant across the globe. An easily obtained, inexpensive, and rapid marker is needed to predict the negative conversion time (NCT) of nucleic acid in nonsevere COVID-19 patients infected by the Omicron variant. This retrospective study enrolled 226 patients infected by the Omicron variant between April 23, 2022, and May 16, 2022. The median age of the patients was 61 (interquartile range (IQR), 48–70) years, and 56.2% were male. 84 patients (37.2%) had at least one comorbidity, and 49 patients (21.7%) were classified into the moderate illness group. 145 patients (64.2%) received at least one dose of vaccine, in which 67 patients (29.6%) received a booster dose of vaccine. The median duration of NCT was 8 (IQR, 7–11) days. Univariate Cox analyses found that high NLR (>2.22), aged ≥65 years, vaccination, and moderate illness were significantly related to the NCT of nucleic acid. Multivariate Cox regression analysis showed that high NLR (NLR > 2.22, hazard ratio (HR):0.718, 95% CI: 0.534–0.964,

p

= 0.028) and vaccination (vaccinated ≥1 dose, HR: 1.536, 95% CI: 1.147–2.058,

p

= 0.004) were independently associated with NCT of nucleic acid. NLR is a rapid, simple, and useful prognostic factor for predicting NCT of nucleic acid in nonsevere COVID-19 patients with the Omicron variant. In addition, vaccination may also play a valuable role in predicting the NCT of nucleic acid.
Cross-talk between PARN and EGFR–STAT3 Signaling Facilitates Self-Renewal and Proliferation of Glioblastoma Stem Cells
Authors: Yin Jinlong , Seo Yoona , Rhim Jiho , Jin Xiong , Kim Tae Hoon , Kim Sung Soo , Hong Jun-Hee , Gwak Ho-Shin , Yoo Heon , Park Jong Bae , Kim Jong Heon 
Published: September 2023

Abstract

Glioblastoma is the most common type of malignant primary brain tumor and displays highly aggressive and heterogeneous phenotypes. The transcription factor STAT3 has been reported to play a key role in glioblastoma malignancy. Thus, discovering targets and functional downstream networks regulated by STAT3 that govern glioblastoma pathogenesis may lead to improved treatment strategies. In this study, we identified that poly(A)-specific ribonuclease (PARN), a key modulator of RNA metabolism, activates EGFR–STAT3 signaling to support glioblastoma stem cells (GSC). Functional integrative analysis of STAT3 found PARN as the top-scoring transcriptional target involved in RNA processing in patients with glioblastoma, and PARN expression was strongly correlated with poor patient survival and elevated malignancy. PARN positively regulated self-renewal and proliferation of GSCs through its 3′–5′ exoribonuclease activity. EGFR was identified as a clinically relevant target of PARN in GSCs. PARN positively modulated EGFR by negatively regulating the EGFR-targeting miRNA miR-7, and increased EGFR expression created a positive feedback loop to increase STAT3 activation. PARN depletion in GSCs reduced infiltration and prolonged survival in orthotopic brain tumor xenografts; similar results were observed using siRNA nanocapsule-mediated PARN targeting. Pharmacological targeting of STAT3 also confirmed PARN regulation by STAT3 signaling. In sum, these results suggest that a STAT3-PARN regulatory network plays a pivotal role in tumor progression and thus may represent a target for glioblastoma therapeutics.

Significance:
A positive feedback loop comprising PARN and EGFR–STAT3 signaling supports self-renewal and proliferation of glioblastoma stem cells to drive tumor progression and can be targeted in glioblastoma therapeutics.
Tamoxifen Response at Single-Cell Resolution in Estrogen Receptor–Positive Primary Human Breast Tumors
Authors: Kim Hyunsoo , Whitman Austin A. , Wisniewska Kamila , Kakati Rasha T. , Garcia-Recio Susana , Calhoun Benjamin C. , Franco Hector L. , Perou Charles M. , Spanheimer Philip M. 
Published: September 2023

Abstract

Purpose:
In estrogen receptor–positive (ER+)/HER2− breast cancer, multiple measures of intratumor heterogeneity are associated with a worse response to endocrine therapy. We sought to develop a novel experimental model to measure heterogeneity in response to tamoxifen treatment in primary breast tumors.

Experimental Design:
To investigate heterogeneity in response to treatment, we developed an operating room-to-laboratory pipeline for the collection of live normal breast specimens and human tumors immediately after surgical resection for processing into single-cell workflows for experimentation and genomic analyses. Live primary cell suspensions were treated ex vivo with tamoxifen (10 μmol/L) or control media for 12 hours, and single-cell RNA libraries were generated using the 10X Genomics droplet-based kit.

Results:
In total, we obtained and processed normal breast tissue from two women undergoing reduction mammoplasty and tumor tissue from 10 women with ER+/HER2− invasive breast carcinoma. We demonstrate differences in tamoxifen response by cell type and identify distinctly responsive and resistant subpopulations within the malignant cell compartment of human tumors. Tamoxifen resistance signatures from resistant subpopulations predict poor outcomes in two large cohorts of ER+ breast cancer patients and are enriched in endocrine therapy–resistant tumors.

Conclusions:
This novel ex vivo model system now provides the foundation to define responsive and resistant subpopulations within heterogeneous human tumors, which can be used to develop precise single cell–based predictors of response to therapy and to identify genes and pathways driving therapeutic resistance.