bluuebunny/crossref_metadata_2025_split huggingface dataset:
Rare variations within the serine/arginine‐rich splicing factor PtoRSZ21 modulate stomatal size to determine drought tolerance in Populus
Authors: Huang Rui , Jin Zhuoying , Zhang Donghai , Li Lianzheng , Zhou Jiaxuan , Xiao Liang , Li Peng , Zhang Mengjiao , Tian Chongde , Zhang Wenke , Zhong Leishi , Quan Mingyang , Zhao Rui , Du Liang , Liu Li‐Jun , Li Zhonghai , Zhang Deqiang , Du Qingzhang 
Published: July 2024

Summary

Rare variants contribute significantly to the ‘missing heritability’ of quantitative traits. The genome‐wide characteristics of rare variants and their roles in environmental adaptation of woody plants remain unexplored.

Utilizing genome‐wide rare variant association study (RVAS), expression quantitative trait loci (eQTL) mapping, genetic transformation, and molecular experiments, we explored the impact of rare variants on stomatal morphology and drought adaptation in Populus.

Through comparative analysis of five world‐wide Populus species, we observed the influence of mutational bias and adaptive selection on the distribution of rare variants. RVAS identified 75 candidate genes correlated with stomatal size (SS)/stomatal density (SD), and a rare haplotype in the promoter of serine/arginine‐rich splicing factor PtoRSZ21 emerged as the foremost association signal governing SS. As a positive regulator of drought tolerance, PtoRSZ21 can recruit the core splicing factor PtoU1‐70K to regulate alternative splicing (AS) of PtoATG2b (autophagy‐related 2). The rare haplotype PtoRSZ21hap2 weakens binding affinity to PtoMYB61, consequently affecting PtoRSZ21 expression and SS, ultimately resulting in differential distribution of Populus accessions in arid and humid climates.

This study enhances the understanding of regulatory mechanisms that underlie AS induced by rare variants and might provide targets for drought‐tolerant varieties breeding in Populus.
Optimal isolation, culture, and in vitro propagation of spermatogonial stem cells in Huaixiang chicken
Authors: Ibtisham Fahar , Tang Shuyan , Song Yiping , Wanze Wang , Xiao Mei , Honaramooz Ali , An Lilong 
Published: July 2024

AbstractSpermatogonial stem cells (SSCs) comprise the foundation of spermatogenesis and hence have great potential for fertility preservation of rare or endangered species and the development of transgenic animals and birds. Yet, developing optimal conditions for the isolation, culture, and maintenance of SSCs in vitro remains challenging, especially for chicken. The objectives of this study were to (1) find the optimal age for SSC isolation in Huaixiang chicken, (2) develop efficient protocols for the isolation, (3) enrichment, and (4) culture of isolated SSCs. In the present study, we first compared the efficiency of SSC isolation using 11 different age groups (8–79 days of age) of Huaixiang chicken. We found that the testes of 21‐day‐old chicken yielded the highest cell viability. Next, we compared two different enzymatic combinations for isolating SSCs and found that 0.125% trypsin and 0.02 g/L EDTA supported the highest number and viability of SSCs. This was followed by investigating optimal conditions for the enrichment of SSCs, where we observed that differential plating had the highest enrichment efficiency compared to the Percoll gradient and magnetic‐activated cell sorting methods. Lastly, to find the optimal culture conditions of SSCs, we compared adding different concentrations of foetal bovine serum (FBS; 2%, 5%, 7%, and 10%) and different concentrations of GDNF, bFGF, or LIF (5, 10, 20, or 30 ng/mL). We found that a combination of 2% FBS and individual growth factors, including GDNF (20 ng/mL), bFGF (30 ng/mL), or LIF (5 ng/mL), best supported the proliferation and colony formation of SSCs. In conclusion, SSCs can be optimally isolated through enzymatic digestion from testes of 21‐day‐old chicken, followed by enrichment using differential plating. Furthermore, adding 2% FBS and optimized concentrations of GFNF, bFGF, or LIF in the culture promotes the proliferation of chicken SSCs.
Cold atmospheric plasma therapy for Malassezia folliculitis: Laboratory investigations and a randomized clinical trial
Authors: Wang Na , Yan Tingting , Mei Xiaole , Liu Jia , Lei Yilong , Yang Chunjun 
Published: July 2024

AbstractBackgroundCurrent treatment options for Malassezia folliculitis (MF) are limited. Recent research has demonstrated the inhibitory effect of cold atmospheric plasma (CAP) on the growth of Malassezia pachydermatis in vitro, suggesting CAP as a potential therapeutic approach for managing MF.ObjectivesThe objective of our study is to assess the in vitro antifungal susceptibility of Malassezia yeasts to CAP. Additionally, we aim to evaluate the efficacy and tolerability of CAP in treating patients with MF.MethodsWe initially studied the antifungal effect of CAP on planktonic and biofilm forms of Malassezia yeasts, using well‐established techniques such as zone of inhibition, transmission electron microscopy, colony count assay and 2,3‐bis(2‐methoxy‐4‐nitro‐5‐sulfophenyl)‐2H‐tetrazolium‐5‐carboxanilide salt assay. Subsequently, a randomized (1:1 ratio), active comparator‐controlled, observer‐blind study was conducted comparing daily CAP therapy versus itraconazole 200 mg/day for 2 weeks in 50 patients with MF. Efficacy outcomes were measured by success rate, negative microscopy rate and changes in Dermatology Life Quality Index (DLQI) and Global Aesthetic Improvement Scale (GAIS) scores. Safety was assessed by monitoring adverse events (AEs) and local tolerability.ResultsIn laboratory investigations, CAP time‐dependently inhibited the growth of Malassezia yeasts in both planktonic and biofilm forms. Forty‐nine patients completed the clinical study. At week 2, success was achieved by 40.0% of subjects in the CAP group versus 58.3% in the itraconazole group (p = 0.199). The negative direct microscopy rates of follicular samples were 56.0% in the CAP group versus 66.7% in the itraconazole group (p = 0.444). No significant differences were found in the proportion of subjects achieving DLQI scores of 0/1 (p = 0.456) or in the GAIS responder rates (p = 0.588) between the two groups. Three patients in the CAP group and one patient in the itraconazole group reported mild AEs.ConclusionCAP demonstrated significant antifungal activity against Malassezia yeasts in vitro and exhibited comparable efficacy to itraconazole in treating MF patients. Without the associated adverse effects of oral antifungal drugs, CAP can be considered a promising and safe treatment modality for MF.
Outcomes of kidney transplant recipients exposed to Chagas disease under Benznidazole prophylaxis. A single center 10‐year experience
Authors: Budel Maria L. , Alegretti Ana P. , Prado Natália P. , Machado Fabiani P. , Bauer Andrea C. , Manfro Roberto C. 
Published: July 2024

AbstractBackgroundChagas disease (ChD) is endemic in many parts of the world and can be transmitted through organ transplantation or reactivated by immunosuppression. Organs from infected donors are occasionally used for transplantation, and the best way of managing the recipients remains a subject of debate.MethodsWe present a single‐center cohort study describing a 10‐year experience of kidney transplantation in patients at risk of donor‐derived ChD and or reactivation. Patients received prophylactic treatment with Benznidazole and were monitored for transmission or reactivation. Monitoring included assessing direct parasitemia, serology, and polymerase chain reaction (PCR).ResultsFifty‐seven kidney transplant recipients (KTRs) were enrolled in the study. Forty‐four patients (77.2%) were at risk of primary ChD infection, nine patients (15.8%) were at risk of disease reactivation, and four patients (7.0%) were at risk of both. All patients received Benznidazole prophylaxis, starting on the first day after transplantation. Parasitemia was assessed in 51 patients (89.5%), serology also in 51 patients (89.5%), and PCR in 40 patients (70.2%). None of the patients exhibited clinically or laboratory‐detectable signs of disease. A single patient experienced a significant side effect, a cutaneous rash with intense pruritus. At 1‐year post‐transplantation, the patient and graft survival rates were 96.5% and 93%, respectively.ConclusionIn this study, no donor‐derived or reactivation of Trypanosoma cruzi infection occurred in KTRs receiving Benznidazole prophylaxis.
Tetrodotoxin‐resistant mechanosensitivity and L‐type calcium channel‐mediated spontaneous calcium activity in enteric neurons
Authors: Amedzrovi Agbesi Richard J. , El Merhie Amira , Spencer Nick J. , Hibberd Tim , Chevalier Nicolas R. 
Published: July 2024

AbstractGut motility undergoes a switch from myogenic to neurogenic control in late embryonic development. Here, we report on the electrical events that underlie this transition in the enteric nervous system, using the GCaMP6f reporter in neural crest cell derivatives. We found that spontaneous calcium activity is tetrodotoxin (TTX) resistant at stage E11.5, but not at E18.5. Motility at E18.5 was characterized by periodic, alternating high‐ and low‐frequency contractions of the circular smooth muscle; this frequency modulation was inhibited by TTX. Calcium imaging at the neurogenic‐motility stages E18.5–P3 showed that CaV1.2‐positive neurons exhibited spontaneous calcium activity, which was inhibited by nicardipine and 2‐aminoethoxydiphenyl borate (2‐APB). Our protocol locally prevented muscle tone relaxation, arguing for a direct effect of nicardipine on enteric neurons, rather than indirectly by its relaxing effect on muscle. We demonstrated that the ENS was mechanosensitive from early stages on (E14.5) and that this behaviour was TTX and 2‐APB resistant. We extended our results on L‐type channel‐dependent spontaneous activity and TTX‐resistant mechanosensitivity to the adult colon. Our results shed light on the critical transition from myogenic to neurogenic motility in the developing gut, as well as on the intriguing pathways mediating electro‐mechanical sensitivity in the enteric nervous system.Highlights
What is the central question of this study?What are the first neural electric events underlying the transition from myogenic to neurogenic motility in the developing gut, what channels do they depend on, and does the enteric nervous system already exhibit mechanosensitivity?
What is the main finding and its importance?ENS calcium activity is sensitive to tetrodotoxin at stage E18.5 but not E11.5. Spontaneous electric activity at fetal and adult stages is crucially dependent on L‐type calcium channels and IP3R receptors, and the enteric nervous system exhibits a tetrodotoxin‐resistant mechanosensitive response.
Abstract figure legend Tetrodotoxin‐resistant Ca2+ rise induced by mechanical stimulation in the E18.5 mouse duodenum.
A summary of the main themes and findings presented at the ASM Intermountain Branch meeting (2024)
Authors: Radke Jay , Ochoa-Repåraz Javier , Nixon Jamee , Acharya Sajal , Bridgewater Haley , Burger Joshua , Cheever Abigail , Darby Robert , Doyle William , Gaur Alka , Githuku Eva , Goodman Rose , Haynie Topher , Hedelius Hannah , Hill Kristina , Iqbal Misha , Laabi Salma , Moreno Carlos , Moss Melinda , Parveen Nagama , Rapier-Sharman Naomi , Sadeghi Sara , Saleh Saeed , Schumacher Sean , Sharp Miranda , Souza Noah , Thapa Soni , Aggabao Shule , Amsbury David , Bautista Sheena Isabelle , Bogh Atalie , Bohn Aaron , Brink Cade , Bryner B. Shaun , Cannon James , Carrington Scot , Chamberlain Hayzen , Cherry Alex , Cole McKaylin , Corrales Edgar , Cullimore Caz , Daines Sophie , Danielson Payson , Domike Monterey , East Matthew , Ellis Bronwyn , Evans Taryn , Fears Zach , Fellars Paige , Fisher Tate , Floyd Braxton , Gibson Trenton , Gueller Mason , Gupta Heather , Gwilliam Jacob , Hansen Mackenzie , Hardy Jacob , Harrell Christopher , Hassell Rebecca , Hendricks Wesley , Hendrix Colby , Henstrom Hirsche , Hernandez Sanguino Kelly , Higgins George , Hwang Hyunbi , Jackson Matt , Jensen Conner , Johnson Austin , Kang Chloe , Kim Sehi , LaFollette Alexandra , Larsen Phoenix , Larson Abbey , Leary Bryson , Longhurst Jayden , Mann Michael , Martinez Isreal , Matthews Brooklyn , McStraw Cody , Mireill Ninahazwe , Moffat Rachel , Mourik Peter , Mudrow Madelyn , Odell Mailon , Oler Blake , Olsen Natalie , Paymard Nazanin , Payne Spencer T. , Pearson Levi , Peter Josh , Peterson Tiffani , Puentes Navarro Daniel , Radke Kyla , Richardson Joseph , Ridd Russell , Rowe Akir , Schmanski Rylan , Scott Jacob , Scott Samuel , Simpkins Mya , Sisk Madalyne , Smith Tyler , Smith Brinley , Sy Jacob , Trejo Gisselle , Van Oostendorp Bartel , Walbom Ethan , Whetten Rebecca , Zollinger Dallin , Braunstein Miriam , Breakwell Donald P. , Chakraborty Anirban , Crook Matthew , Culumber Michele , Hatch Wayne , Jimenez Victor M. , Nematollahi Wales P. , Olson Michael , Poritz Mark , Ririe Seth , Schachterle Jeffrey , Wiltbank Lisa , Kelson Todd , Pickett Brett E. 
Published: July 2024

ABSTRACT

The annual meeting for the Intermountain Branch was held in April 2024 on the campus of Brigham Young University. There were 127 branch members from Utah, Idaho, and Nevada who attended the meeting and were composed of undergraduate students, graduate or medical students, and faculty. This report highlights the diversity of, and the emerging trends in, the research conducted by American Society for Microbiology members in the Intermountain Branch.
Metagenomic clustering links specific metabolic functions to globally relevant ecosystems
Authors: Flinkstrom Zachary , Bryson Samuel , Candry Pieter , Winkler Mari-Karoliina H. 
Published: July 2024

ABSTRACT

Metagenomic sequencing has advanced our understanding of biogeochemical processes by providing an unprecedented view into the microbial composition of different ecosystems. While the amount of metagenomic data has grown rapidly, simple-to-use methods to analyze and compare across studies have lagged behind. Thus, tools expressing the metabolic traits of a community are needed to broaden the utility of existing data. Gene abundance profiles are a relatively low-dimensional embedding of a metagenome’s functional potential and are, thus, tractable for comparison across many samples. Here, we compare the abundance of KEGG Ortholog Groups (KOs) from 6,539 metagenomes from the Joint Genome Institute’s Integrated Microbial Genomes and Metagenomes (JGI IMG/M) database. We find that samples cluster into terrestrial, aquatic, and anaerobic ecosystems with marker KOs reflecting adaptations to these environments. For instance, functional clusters were differentiated by the metabolism of antibiotics, photosynthesis, methanogenesis, and surprisingly GC content. Using this functional gene approach, we reveal the broad-scale patterns shaping microbial communities and demonstrate the utility of ortholog abundance profiles for representing a rapidly expanding body of metagenomic data.

IMPORTANCE
Metagenomics, or the sequencing of DNA from complex microbiomes, provides a view into the microbial composition of different environments. Metagenome databases were created to compile sequencing data across studies, but it remains challenging to compare and gain insight from these large data sets. Consequently, there is a need to develop accessible approaches to extract knowledge across metagenomes. The abundance of different orthologs (i.e., genes that perform a similar function across species) provides a simplified representation of a metagenome’s metabolic potential that can easily be compared with others. In this study, we cluster the ortholog abundance profiles of thousands of metagenomes from diverse environments and uncover the traits that distinguish them. This work provides a simple to use framework for functional comparison and advances our understanding of how the environment shapes microbial communities.
Identification and characterization of a skin microbiome on
Caenorhabditis elegans
suggests environmental microbes confer cuticle protection
Authors: Haghani Nadia B. , Lampe Robert H. , Samuel Buck S. , Chalasani Sreekanth H. , Matty Molly A. 
Published: July 2024

ABSTRACT

In the wild,
C. elegans
are emersed in environments teeming with a veritable menagerie of microorganisms. The
C. elegans
cuticular surface serves as a barrier and first point of contact with their microbial environments. In this study, we identify microbes from
C. elegans
natural habitats that associate with its cuticle, constituting a simple “skin microbiome.” We rear our animals on a modified CeMbio, mCeMbio, a consortium of ecologically relevant microbes. We first combine standard microbiological methods with an adapted micro skin-swabbing tool to describe the skin-resident bacteria on the
C. elegans
surface. Furthermore, we conduct 16S rRNA gene sequencing studies to identify relative shifts in the proportion of mCeMbio bacteria upon surface-sterilization, implying distinct skin- and gut-microbiomes. We find that some strains of bacteria, including
Enterobacter
sp. JUb101
,
are primarily found on the nematode skin, while others like
Stenotrophomonas indicatrix
JUb19 and
Ochrobactrum vermis
MYb71 are predominantly found in the animal’s gut. Finally, we show that this skin microbiome promotes host cuticle integrity in harsh environments. Together, we identify a skin microbiome for the well-studied nematode model and propose its value in conferring host fitness advantages in naturalized contexts.

IMPORTANCE

The genetic model organism
C. elegans
has recently emerged as a tool for understanding host–microbiome interactions. Nearly all of these studies either focus on pathogenic or gut-resident microbes. Little is known about the existence of native, nonpathogenic skin microbes or their function. We demonstrate that members of a modified
C. elegans
model microbiome, mCeMbio, can adhere to the animal's cuticle and confer protection from noxious environments. We combine a novel micro-swab tool, the first 16S microbial sequencing data from relatively unperturbed
C. elegans
, and physiological assays to demonstrate microbially mediated protection of the skin. This work serves as a foundation to explore wild
C. elegans
skin microbiomes and use
C. elegans
as a model for skin research.
Sacbrood viruses and select Lake Sinai virus variants dominated
Apis mellifera
colonies symptomatic for European foulbrood
Authors: Hesketh-Best Poppy J. , Fowler Peter D. , Odogwu Nkechi M. , Milbrath Meghan O. , Schroeder Declan C. 
Published: July 2024

ABSTRACT

European foulbrood (EFB) is a prevalent disease in the European honey bee (
Apis mellifera
) in the United States, which can lead to colony decline and collapse. The bacterial components of EFB are well-studied, but the diversity of viral infections within infected colonies has not been explored. In this study, we use meta-transcriptomics sequencing of 12 honey bee hives, symptomatic (+,
n
= 6) and asymptomatic (–,
n
= 6) for EFB, to investigate viral infection associated with the disease. We assembled 41 viral genomes, belonging to three families (Iflaviridae, Dicistroviridae, and Sinhaliviridae), all previously reported in honey bees, including Lake Sinai virus, deformed wing virus, sacbrood virus, Black queen cell virus, and Israeli acute paralysis virus. In colonies with severe EFB, we observed a higher occurrence of viral genomes (34 genomes) in contrast to fewer recovered from healthy colonies (seven genomes) and a complete absence of Dicistroviridae genomes.We observed specific Lake Sinai virus clades associated exclusively with EFB + or EFB – colonies, in addition to EFB-afflicted colonies that exhibited an increase in relative abundance of sacbrood viruses. Multivariate analyses highlighted that a combination of site and EFB disease status influenced RNA virome composition, while EFB status alone did not significantly impact it, presenting a challenge for comparisons between colonies kept in different yards. These findings contribute to the understanding of viral dynamics in honey bee colonies compromised by EFB and underscore the need for future investigations to consider viral composition when investigating EFB.

IMPORTANCE
This study on the viromes of honey bee colonies affected by European foulbrood (EFB) sheds light on the dynamics of viral populations in bee colonies in the context of a prevalent bacterial brood disease. The identification of distinct Lake Sinai virus and sacbrood virus clades associated with colonies affected by severe EFB suggests a potential connection between viral composition and disease status, emphasizing the need for further investigation into the role of viruses during EFB infection. The observed increase in sacbrood viruses during EFB infection suggests a potential viral dysbiosis, with potential implications for honey bee brood health. These findings contribute valuable insights related to beekeeping practices, offering a foundation for future research aimed at understanding and mitigating the impact of bacterial and viral infection in commercial honey bee operations and the management of EFB.
Immunogenicity and vaccine potential of clinical isolate
Mycobacterium kansasii
strain against
Mycobacterium tuberculosis
infection
Authors: Kim Hongmin , Shin Sung Jae 
Published: July 2024

ABSTRACT

Mycobacterium kansasii
is a bacterium included in non-tuberculous mycobacteria (NTM) that can cause lung disease. It shares a significant number of antigens with
Mycobacterium tuberculosis
(Mtb), suggesting that it has the potential to be used as a tuberculosis (TB) vaccine. Therefore, we subcutaneously vaccinated mice with reference strain,
M. kansasii
-ATCC12478 [
M. kansasii
-American Type Culture Collection (ATCC)], and clinically isolated strain,
M. kansasii
-SM-1 to evaluate potential as a TB vaccine by comparing with bacille Calmette-Guerin (BCG) vaccine. Ten weeks after vaccination, we evaluated immunogenicity of
M. kansasii
-ATCC and
M. kansasii
-SM-1, and
M. kansasii
-SM-1 immunization induces potent Mtb antigen-specific IFN-γ-producing CD4
+
T cells than
M. kansasii
-ATCC. Upon Mtb infection,
M. kansasii
-SM-1 provided better protection than
M. kansasii
-ATCC, which was comparable to the efficacy of BCG. These results showed that the clinical strain
M. kansasii
-SM-1, which exhibits an enhanced Mtb antigen-specific Th1 response, shows greater vaccine efficacy compared to
M. kansasii
-ATCC. In this study, we demonstrated that vaccine efficacy can vary depending on the strain of
M. kansasii
and that its efficacy can be comparable to BCG. This suggests that
M. kansasii
has the potential to be a live TB vaccine candidate.

IMPORTANCE

Mycobacterium kansasii
, a non-tuberculous mycobacteria (NTM) species causing lung disease, shares key antigens with
Mycobacterium tuberculosis
(Mtb), indicating its potential for TB vaccine development. Subcutaneous vaccination of mice with
M. kansasii
strains reference strain
M. kansasii
-ATCC12478 [(
M. kansasii
-American Type Culture Collection (ATCC)] and clinically isolated strain
M. kansasii
-SM-1 revealed differences in immunogenicity.
M. kansasii
-SM-1 induced a robust Mtb antigen-specific IFN-γ-producing CD4
+
T cell response compared to
M. kansasii
-ATCC. Additionally,
M. kansasii
-SM-1 conferred better protection against Mtb infection than
M. kansasii
-ATCC, which is comparable to bacille Calmette-Guerin (BCG). These findings underscore the variable vaccine efficacy among
M. kansasii
strains, with
M. kansasii
-SM-1 exhibiting promising potential as a live TB vaccine candidate, suggesting its comparative effectiveness to BCG.