bluuebunny/crossref_metadata_2025 huggingface dataset:
Topical Use of Low‐dose Tranexamic Acid Has no Effect on Drainage Volume after Medial Open Wedge High Tibial Osteotomy: A Case Control Study
Authors: Zheng Huifeng , Han Yuqin , Zhao Guangjuan , Wang Rui , Wu Jiang , Chen Xiao , Zhao Qian , Ren Fuji , Huang Jingmin
Published: March 2024

Objective

Many studies reported that tranexamic acid (TXA) was effective in reducing surgical blood loss in the perioperative period of medial open wedge high tibial osteotomy (MOWHTO). However, few studies focused on the simple topical use of TXA in MOWHTO, and the modality and dosage of topical use of TXA varied. The purpose of this study was to observe the effect of topical use of low‐dose TXA on drainage volume after MOWHTO, and to analyze the related influencing factors.

Methods

Data of patients who underwent MOWHTO combined with arthroscopic knee surgery in our department from January 2019 to September 2021 were retrospectively analyzed. A total of 105 patients (38 males and 67 females, aged 57.7 ± 7.5 years) were included in this study who received topical TXA or no TXA. The patients were divided into three groups: control group (39 cases), 0.5 g TXA group (40 cases), 1 g TXA group (26 cases). Postoperative drainage volume, wound healing, incidence of hematoma and deep venous thrombosis (DVT) were observed and analyzed in the three groups. The effects of gender, hypertension and diabetes on postoperative drainage volume were analyzed using a t‐test. The correlation between age, body mass index (BMI), osteotomy gap and postoperative drainage volume were analyzed using the Pearson correlation coefficient.

Results

The average postoperative drainage volume of the control group was 259.54 ± 226.33 mL, that of the 0.5 g TXA group was 277.18 ± 177.68 mL, and that of the 1 g TXA group was 229.15 ± 219.93 mL. There was no statistically significant difference in postoperative drainage volume among the three groups (F = 0.423, p = 0.656). There was no local hematoma and wound infection in the three groups. The wound fat liquefaction was found in one patient of the control group. The incidence of DVT was 38.9% (7/18) and 57.1% (8/14) in the control group and 0.5 TXA group, respectively. There was no significant difference in the incidence of DVT between the above two groups (p = 0.476). The average postoperative drainage volume of male patients in the three groups was higher than that of female patients, and the differences were statistically significant (p < 0.05). There was no correlation between age, BMI, osteotomy gap and postoperative drainage volume in the three groups (p > 0.05).

Conclusion

Topical use of low‐dose TXA has no significant effect on drainage volume after MOWHTO. The drainage volume after MOWHTO in male patients was more than that in female patients. Topical administration of low‐dose TXA does not increase postoperative complications, such as DVT and hematoma.
Phylogenetics and phylogeography of Euphorbia canariensis reveal an extreme Canarian‐Asian disjunction but limited inter‐island colonization
Authors: Coello A. J. , Vargas P. , Cano E. , Riina R. , Fernández‐Mazuecos M.
Published: March 2024

Euphorbia canariensis is an iconic endemic species representative of the lowland xerophytic communities of the Canary Islands. It is widely distributed in the archipelago despite having diasporas unspecialized for long‐distance dispersal. Here, we reconstructed the evolutionary history of E. canariensis at two levels: a time‐calibrated phylogenetic analysis aimed at clarifying interspecific relationships and large‐scale biogeographic patterns; and a phylogeographic study focused on the history of colonization across the Canary Islands.

For the phylogenetic study, we sequenced the ITS region for E. canariensis and related species of Euphorbia sect. Euphorbia. For the phylogeographic study, we sequenced two cpDNA regions for 28 populations representing the distribution range of E. canariensis. The number of inter‐island colonization events was explored using PAICE, a recently developed method that includes a sample size correction. Additionally, we used species distribution modelling (SDM) to evaluate environmental suitability for E. canariensis through time.

Phylogenetic results supported a close relationship between E. canariensis and certain Southeast Asian species (E. epiphylloides, E. lacei, E. sessiliflora). In the Canaries, E. canariensis displayed a west‐to‐east colonization pattern, not conforming to the “progression rule”, i.e. the concordance between phylogeographic patterns and island emergence times. We estimated between 20 and 50 inter‐island colonization events, all of them in the Quaternary, and SDM suggested a late Quaternary increase in environmental suitability for E. canariensis.

The extreme biogeographic disjunction between Macaronesia and Southeast Asia (ca. 11,000 km) parallels that found in a few other genera (Pinus, Dracaena). We hypothesize that these disjunctions are better explained by extinction across north Africa and southwest Asia rather than long‐distance dispersal. The relatively low number of inter‐island colonization events across the Canaries is congruent with the low dispersal capabilities of E. canariensis.
The impact of energy prices on inflation and economic growth in Mozambique: A wavelet approach and OLS estimator
Authors: da Conceição Gilmar Fernando Dias
Published: March 2024

The paper is using the Continuous Wavelet Transform (CWT) and the OLS estimator to examine the relationship between energy prices (coal and gas), inflation and economic growth in Mozambique. Coal and gas are the primary commodity and source of revenue for the country. The research uses quarterly data from 2001 to 2022. Among other results, we found evidence of high coherence between macroeconomic variables (inflation and real GDP growth rate) and energy prices (thermal coal and natural gas prices) only for the frequency intervals between 1.5 and 4 years (short term). The results hold even after controlling for the real GDP growth and exchange rate; we concluded that only in the short term (1.5–4 years), there is high coherence between energy prices and inflation in the time interval between 2004 and 2012. This finding indicates no relation between energy prices, inflation and economic growth in Mozambique. Furthermore, the OLS estimates substantiate the wavelet result, showing no impact. In this context, we can conclude that there is probably a ‘Dutch disease’ or ‘resource curse’ that negates the positive effects of exploiting these resources on short‐ and long‐term economic growth.
Biochar amendment gradually immobilized soil As and Sb over 2 years
Authors: Hu Ying , Wang Liuwei , Mašek Ondřej , Chen Bei , Xu Yuanyuan , Liang Peng , Hou Deyi
Published: March 2024

Biochar is a promising candidate for the sustainable remediation of soils, especially those contaminated with cationic heavy metals, because of its liming effect and tunable surface functionality. Despite its potential, prior studies have highlighted biochar's limitations in immobilizing soil oxyanions, such as arsenic (As) and antimony (Sb), particularly in the short term. This shotcoming is primarily attributed to an increase of soil pH following biochar amendment, and factors like competition with phosphate. In this study, biochar amendments were applied to three soils with varying levels of oxyanions including As and Sb, and cations including cadmium (Cd) and lead (Pb). These treatments generally resulted in short‐term failure of oxyanion immobilization. However, a noteworthy phenomenon unfolded over a 2‐year period, where biochars gradually transitioned from initial mobilization or poor immobilization to eventual successful immobilization of oxyanions (up to 87.0% for As and 100% for Sb). Temporal changes in Cd and Pb differed from As and Sb, exhibiting no improvement in immobilization rates over time. Potential mechanisms driving this process were investigated, suggesting a decline in soil pH, progressive oxidation of soil carbon fractions, and direct adsorption effects as contributing factors. This study sheds light on the temporal shift in biochar's immobilization performance, highlighting a gradual increase in the efficacy in oxyanion immobilization. The findings offer valuable insights into the dynamic nature of biochar's remediation capabilities.
Measuring and modelling the impact of outdoor pigs on soil carbon and nutrient dynamics under a changing climate and different management scenarios
Authors: Pun I. , Galdos M. V. , Chapman P. J. , Lloyd I. L. , Banwart S. , Dobbie S. , Collins L.
Published: March 2024

A mixed agricultural system that integrates livestock and cropping is essential to organic, agroecological, and regenerative farming. The demand for improved welfare systems has made the practice of outdoor rearing of pigs very popular; it currently makes up 40% of the UK pig industry and has also been integrated into arable rotations. Besides the benefits of outdoor production systems, they also potentially pose environmental risks to farmlands, such as accumulation of nitrogen and phosphorus in the soil, soil erosion and compaction and carbon loss. Despite this, the impact of outdoor pigs and arable crop rotations on soil health has been under‐researched relative to other livestock species. This study was conducted at the University of Leeds Research Farm from 2018 to 2020 using a combined experimental and modelling approach to understand the impact of outdoor pigs on soil carbon and nutrient dynamics. The physio‐chemical properties of arable soil were measured prior to the introduction of the pigs and after introducing the pigs at the end of first and second years, consecutively. There was assessment of control sites (without pigs, mowing once a year) and pig pens (pigs in a rotation with arable crops). The soil was sampled at two different depths, 0–10 cm and 10–20 cm. It was observed that measured soil organic carbon (SOC) stocks in the soil depths of 0–10 cm and 10–20 cm layer were decreased by 7% and 3%, respectively, in the pig pens from 2019 to 2020, and total available nitrogen and phosphorus were significantly higher in pig pens than the control sites. Hence, at a depth between 0 and 20 cm, the average total available nitrogen was 2.51 and 2.68 mg kg−1 in the control sites and 21.76 and 20.45 mg kg−1 in the pig pens in 2019 and 2020, respectively. The average total available phosphorus at 0–20 cm was 26.54 and 37.02 mg kg−1 in control sites and 48.15 and 63.58 mg kg−1 in pig pens during 2019 and 2020, respectively. A process‐based model (DayCent) was used to simulate soil carbon and nitrogen dynamics in the arable rotation with outdoor pigs and showed SOC stock losses of – 0.09 ± 0.23 T C ha−1 year−1 using the future climate CMIP5 RCP 8.5 scenario for 2020 to 2048. To reduce this loss, we modelled the impact of changing the management of the pig rotation and found that the loss of SOC stock could be decreased by shortening the period of pig retention in the field, growing grass in the field, and leguminous crops in the crop rotation.
Performance time and leak pressure of hand‐sewn and skin staple intestinal anastomoses and enterotomies in cadaveric cats
Authors: Miller Annellie K. , Regier Penny J. , Collins Maggie C. , Rivas Marc A. , Colee James C.
Published: March 2024

Objective

To compare time to construct completion and leak testing between hand‐sewn and skin staple anastomoses and enterotomies in cats.

Study design

Ex vivo, randomized study.

Animals

Fresh feline cadavers (n = 20).

Methods

Jejunal segments (8 cm) were harvested and tested on the same day as euthanasia. From each cadaver, one segment was randomly assigned to control (C), hand‐sewn enterotomy (HSE), and skin staple enterotomy (SSE) groups, and two segments were randomly assigned to hand‐sewn anastomosis (HSA) and skin staple anastomosis (SSA) groups. Construct completion time, initial leak pressure (ILP), and maximum intraluminal pressure were compared. Leakage location was reported.

Results

Mean time (s) ± SD was longer (p < .001) for HSA (317.0 ± 50.9) than SSA (160.8 ± 13.1) and for HSE (172.0 ± 36.5) than SSE (20.3 ± 5.0). ILP (mean ± SD) for C (600.0 mmHg ±0.0) was higher (p < .001) than all constructs. ILP (mean ± SD) for SSA (124.2 mmHg ±83.7) was not different (p = .49) than HSA (86.1 ± 51.9), but HSE (200.3 ± 114.7) was higher (p < .001) than SSE (32.2 ± 39.7). Immediate leakage from the center of enterotomy closure was observed in 7/20 SSE.

Conclusions

HSA construct completion took twice as long as SSA with no difference in intraluminal pressures. Although HSE construct completion took 8x as long as SSE, HSE had higher intraluminal pressures.

Clinical significance

In cats, SSA may be an alternative to HSA for intestinal anastomosis, but SSE is not recommended as an alternative to HSE for intestinal enterotomy closure.
Nucleation of highly uniform AlN thin films by high volume batch ALD on 200 mm platform
Authors: Mukhopadhyay Partha , Fletcher Ivan , Caribe Couvertier Zuriel , Schwab Brent , Gumpher John , Schoenfeld Winston V. , Kretzschmar Jon , deVilliers Anton , Fulford Jim
Published: March 2024

A highly uniform aluminum nitride thin film has been developed by thermal atomic layer deposition (ALD), which is designed to handle high volume of 200 mm wafers. A three-sigma thickness variation of <0.5 Å resulted from repeatable batch depositions of over 500 Å, while wafer-within-wafer (WinW) and wafer-to-wafer (WtoW) remained <5% by the optimized recipe in a 100+ wafer reactor. Various ALD deposition temperatures, film thicknesses, and substrate types of Si, quartz, and GaN/Si(111) templates have been examined for material and optical properties of an AlN film. A narrow temperature window of 300–350 °C was identified as the most suitable for the deposition process with 350 °C as the optimized one. Substrate-inhibited growth and nonlinearity in deposition rate have been observed for AlN which is possibly related to the available reaction sites at the time of nucleation on foreign substrate surfaces. A special set of experiments with a thorough exploration of XPS individual peaks such as Al2p, N1s, C1s, and O1s reveals negligible carbon and oxygen contamination with cent-percent Al–N bonding. An amorphous AlN film is evident on Si by cross-sectional TEM while a trace of polycrystalline film on GaN templates with smooth heterointerfaces to AlGaN/GaN structures. The optical bandgap is estimated to be 5.8 eV from the transmittance experiment. An in-depth refractive-index investigation shows high-density AlN by TEL Alpha-8SEiTM batch ALD which also exhibits excellent uniformity over composition and thickness with run-to-run (RtoR), WtoW, and WinW uniformity under 0.5%, highlighting the reliability and precision of the process while having high throughput.
Effects of contralateral noise on envelope-following responses, auditory-nerve compound action potentials, and otoacoustic emissions measured simultaneously
Authors: Faubion Shelby L. , Park Ryan K. , Lichtenhan Jeffery T. , Jennings Skyler G.
Published: March 2024

This study assessed whether the effects of contralateral acoustic stimulation (CAS) are consistent with eliciting the medial olivocochlear (MOC) reflex for measurements sensitive to outer hair cell (otoacoustic emissions, OAEs), auditory-nerve (AN; compound action potential, CAP), and brainstem/cortical (envelope-following response, EFR) function. The effects of CAS were evaluated for simultaneous measurement of OAEs, CAPs, and EFRs in participants with normal hearing. Clicks were presented at 40 or 98 Hz in three ipsilateral noise conditions (no noise, 45 dB SPL, and 55 dB SPL). For the no noise condition, CAS suppressed or enhanced EFR amplitudes for 40- and 98-Hz clicks, respectively, while CAS had no significant effect on CAP amplitudes. A follow-up experiment using slower rates (4.4–22.2 Hz) assessed whether this insignificant CAS effect on CAPs was from ipsilateral MOC stimulation or AN adaptation; however, CAS effects remained insignificant despite favorable signal-to-noise ratios. CAS-related enhancements of EFR and CAP amplitudes in ipsilateral noise were not observed, contrary to the anti-masking effect of the MOC reflex. EFR and OAE suppression from CAS were not significantly correlated. Thus, the effects of CAS on EFRs may not be solely mediated by the MOC reflex and may be partially mediated by higher auditory centers.
Machine learning predictions of T cell antigen specificity from intracellular calcium dynamics
Authors: This Sébastien , Costantino Santiago , Melichar Heather J.
Published: March 2024

Adoptive T cell therapies rely on the production of T cells with an antigen receptor that directs their specificity toward tumor-specific antigens. Methods for identifying relevant T cell receptor (TCR) sequences, predominantly achieved through the enrichment of antigen-specific T cells, represent a major bottleneck in the production of TCR-engineered cell therapies. Fluctuation of intracellular calcium is a proximal readout of TCR signaling and candidate marker for antigen-specific T cell identification that does not require T cell expansion; however, calcium fluctuations downstream of TCR engagement are highly variable. We propose that machine learning algorithms may allow for T cell classification from complex datasets such as polyclonal T cell signaling events. Using deep learning tools, we demonstrate accurate prediction of TCR-transgenic CD8
+
T cell activation based on calcium fluctuations and test the algorithm against T cells bearing a distinct TCR as well as polyclonal T cells. This provides the foundation for an antigen-specific TCR sequence identification pipeline for adoptive T cell therapies.
Sex differences in kidney metabolism may reflect sex-dependent outcomes in human diabetic kidney disease
Authors: Clotet-Freixas Sergi , Zaslaver Olga , Kotlyar Max , Pastrello Chiara , Quaile Andrew T. , McEvoy Caitriona M. , Saha Aninda D. , Farkona Sofia , Boshart Alex , Zorcic Katarina , Neupane Slaghaniya , Manion Kieran , Allen Maya , Chan Michael , Chen Xuqi , Arnold Arthur P. , Sekula Peggy , Steinbrenner Inga , Köttgen Anna , Dart Allison B. , Wicklow Brandy , McGavock Jon M. , Blydt-Hansen Tom D. , Barrios Clara , Riera Marta , Soler María J. , Isenbrandt Amandine , Lamontagne-Proulx Jérôme , Pradeloux Solène , Coulombe Katherine , Soulet Denis , Rajasekar Shravanthi , Zhang Boyang , John Rohan , Mehrotra Aman , Gehring Adam , Puhka Maija , Jurisica Igor , Woo Minna , Scholey James W. , Röst Hannes , Konvalinka Ana
Published: March 2024

Diabetic kidney disease (DKD) is the main cause of chronic kidney disease (CKD) and progresses faster in males than in females. We identify sex-based differences in kidney metabolism and in the blood metabolome of male and female individuals with diabetes. Primary human proximal tubular epithelial cells (PTECs) from healthy males displayed increased mitochondrial respiration, oxidative stress, apoptosis, and greater injury when exposed to high glucose compared with PTECs from healthy females. Male human PTECs showed increased glucose and glutamine fluxes to the TCA cycle, whereas female human PTECs showed increased pyruvate content. The male human PTEC phenotype was enhanced by dihydrotestosterone and mediated by the transcription factor HNF4A and histone demethylase KDM6A. In mice where sex chromosomes either matched or did not match gonadal sex, male gonadal sex contributed to the kidney metabolism differences between males and females. A blood metabolomics analysis in a cohort of adolescents with or without diabetes showed increased TCA cycle metabolites in males. In a second cohort of adults with diabetes, females without DKD had higher serum pyruvate concentrations than did males with or without DKD. Serum pyruvate concentrations positively correlated with the estimated glomerular filtration rate, a measure of kidney function, and negatively correlated with all-cause mortality in this cohort. In a third cohort of adults with CKD, male sex and diabetes were associated with increased plasma TCA cycle metabolites, which correlated with all-cause mortality. These findings suggest that differences in male and female kidney metabolism may contribute to sex-dependent outcomes in DKD.
Identification and characterization of a fungal cutinase-like enzyme CpCut1 from
Cladosporium
sp. P7 for polyurethane degradation
Authors: Liu Jiawei , Xin Kaiyuan , Zhang Tianyang , Wen Yuan , Li Ding , Wei Ren , Zhou Jie , Cui Zhongli , Dong Weiliang , Jiang Min
Published: March 2024

Plastic degradation by biological systems emerges as a prospective avenue for addressing the pressing global concern of plastic waste accumulation. The intricate chemical compositions and diverse structural facets inherent to polyurethanes (PU) substantially increase the complexity associated with PU waste management. Despite the extensive research endeavors spanning over decades, most known enzymes exhibit a propensity for hydrolyzing waterborne PU dispersion (i.e., the commercial Impranil DLN-SD), with only a limited capacity for the degradation of bulky PU materials. Here, we report a novel cutinase (CpCut1) derived from
Cladosporium
sp. P7, which demonstrates remarkable efficiency in the degrading of various polyester-PU materials. After 12-h incubation at 55°C, CpCut1 was capable of degrading 40.5% and 20.6% of thermoplastic PU film and post-consumer foam, respectively, while achieving complete depolymerization of Impranil DLN-SD. Further analysis of the degradation intermediates suggested that the activity of CpCut1 primarily targeted the ester bonds within the PU soft segments. The versatile performance of CpCut1 against a spectrum of polyester-PU materials positions it as a promising candidate for the bio-recycling of waste plastics.

IMPORTANCE

Polyurethane (PU) has a complex chemical composition that frequently incorporates a variety of additives, which poses significant obstacles to biodegradability and recyclability. Recent advances have unveiled microbial degradation and enzymatic depolymerization as promising waste PU disposal strategies. In this study, we identified a gene encoding a cutinase from the PU-degrading fungus
Cladosporium
sp. P7, which allowed the expression, purification, and characterization of the recombinant enzyme CpCut1. Furthermore, this study identified the products derived from the CpCut1 catalyzed PU degradation and proposed its underlying mechanism. These findings highlight the potential of this newly discovered fungal cutinase as a remarkably efficient tool in the degradation of PU materials.
Composting reduces the risks of resistome in beef cattle manure at the transcriptional level
Authors: Sun Yuepeng , Staley Zachery R. , Woodbury Bryan , Riethoven Jean-Jack , Li Xu
Published: March 2024

Transcriptomic evidence is needed to determine whether composting is more effective than conventional stockpiling in mitigating the risk of resistome in livestock manure. The objective of this study is to compare composting and stockpiling for their effectiveness in reducing the risk of antibiotic resistance in beef cattle manure. Samples collected from the center and the surface of full-size manure stockpiling and composting piles were subject to metagenomic and metatranscriptomic analyses. While the distinctions in resistome between stockpiled and composted manure were not evident at the DNA level, the advantages of composting over stockpiling were evident at the transcriptomic level in terms of the abundance of antibiotic resistance genes (ARGs), the number of ARG subtypes, and the prevalence of high-risk ARGs (i.e., mobile ARGs associated with zoonotic pathogens). DNA and transcript contigs show that the pathogen hosts of high-risk ARGs included
Escherichia coli
O157:H7 and O25b:H4,
Klebsiella pneumoniae
, and Salmonella enterica. Although the average daily temperatures for the entire composting pile exceeded 55°C throughout the field study, more ARG and ARG transcripts were removed at the center of the composting pile than at the surface. This work demonstrates the advantage of composting over stockpiling in reducing ARG risk in active populations in beef cattle manure.

IMPORTANCE

Proper treatment of manure before land application is essential to mitigate the spread of antibiotic resistance in the environment. Stockpiling and composting are two commonly used methods for manure treatment. However, the effectiveness of composting in reducing antibiotic resistance in manure has been debated. This work compared the ability of these two methods to reduce the risk of antibiotic resistance in beef cattle manure. Our results demonstrate that composting reduced more high-risk resistance genes at the transcriptomic level in cattle manure than conventional stockpiling. This finding not only underscores the effectiveness of composting in reducing antibiotic resistance in manure but also highlights the importance of employing RNA analyses alongside DNA analyses.
Directed evolution of the fluorescent protein CGP with
in situ
biosynthesized noncanonical amino acids
Authors: Yang Yanhong , Zhang Jing , Yang Jian , Luo Huiwen , Sun Yingjie , Ke Famin , Wang Qin , Gao Xiaowei
Published: March 2024

The incorporation of noncanonical amino acids (ncAAs) into proteins can enhance their function beyond the abilities of canonical amino acids and even generate new functions. However, the ncAAs used for such research are usually chemically synthesized, which is expensive and hinders their application on large industrial scales. We believe that the biosynthesis of ncAAs using metabolic engineering and their employment
in situ
in target protein engineering with genetic code expansion could overcome these limitations. As a proof of principle, we biosynthesized four ncAAs, O-L-methyltyrosine, 3,4-dihydroxy-L-phenylalanine, 5-hydroxytryptophan, and 5-chloro-L-tryptophan using metabolic engineering and directly evolved the fluorescent consensus green protein (CGP) by combination with nine other exogenous ncAAs in
Escherichia coli
. After screening a TAG scanning library expressing 13 ncAAs, several variants with enhanced fluorescence and stability were identified. The variants CGP
V3pMeoF/K190pMeoF
and CGP
G20pMeoF/K190pMeoF
expressed with biosynthetic O-L-methyltyrosine showed an approximately 1.4-fold improvement in fluorescence compared to the original level, and a 2.5-fold improvement in residual fluorescence after heat treatment. Our results demonstrated the feasibility of integrating metabolic engineering, genetic code expansion, and directed evolution in engineered cells to employ biosynthetic ncAAs in protein engineering. These results could further promote the application of ncAAs in protein engineering and enzyme evolution.

IMPORTANCE

Noncanonical amino acids (ncAAs) have shown great potential in protein engineering and enzyme evolution through genetic code expansion. However, in most cases, ncAAs must be provided exogenously during protein expression, which hinders their application, especially when they are expensive or have poor cell membrane penetration. Engineering cells with artificial metabolic pathways to biosynthesize ncAAs and employing them
in situ
for protein engineering and enzyme evolution could facilitate their application and reduce costs. Here, we attempted to evolve the fluorescent consensus green protein (CGP) with biosynthesized ncAAs. Our results demonstrated the feasibility of using biosynthesized ncAAs in protein engineering, which could further stimulate the application of ncAAs in bioengineering and biomedicine.
Refermentation and maturation of lambic beer in bottles: a necessary step for gueuze production
Authors: Bongaerts Dries , Bouchez Arne , De Roos Jonas , Cnockaert Margo , Wieme Anneleen D. , Vandamme Peter , Weckx Stefan , De Vuyst Luc
Published: March 2024

The production of gueuze beers through refermentation and maturation of blends of lambic beer in bottles is a way for lambic brewers to cope with the variability among different lambic beer batches. The resulting gueuze beers are more carbonated than lambic beers and are supposed to possess a unique flavor profile that varies over time. To map this refermentation and maturation process for gueuze production, a blend of lambic beers was made and bottled, whereby one of them was produced with the old wheat landrace
Zeeuwse Witte
. Through the use of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry and high-throughput sequencing of bacterial and fungal amplicons, in combination with metabolite target analysis, new insights into gueuze production were obtained. During the initial stages of refermentation, the conditions in the bottles were similar to those encountered during the maturation phase of lambic beer productions in wooden barrels, which was also reflected microbiologically (presence of
Brettanomyces
species,
Pediococcus damnosus
, and
Acetobacter lambici
) and biochemically (ethanol, higher alcohols, lactic acid, acetic acid, volatile phenolic compounds, and ethyl esters). However, after a few weeks of maturation, a switch from a favorable environment to one with nutrient and dissolved oxygen depletion resulted in several changes. Concerning the microbiology, a sequential prevalence of three lactic acid bacterial species occurred, namely,
P. damnosus
,
Lentilactobacillus buchneri
, and
Lactobacillus acetotolerans
, while the diversity of the yeasts decreased. Concerning the metabolites produced, mainly those of the
Brettanomyces
yeasts determined the metabolic profiles encountered during later stages of the gueuze production.

IMPORTANCE

Gueuze beers are the result of a refermentation and maturation process of a blend of lambic beers carried out in bottles. These gueuze beers are known to have a long shelf life, and their quality typically varies over time. However, knowledge about gueuze production in bottles is scarce. The present study provided more insights into the varying microbial and metabolite composition of gueuze beers during the first 2 years of this refermentation and maturation process. This will allow gueuze producers to gain more information about the influence of the refermentation and maturation time on their beers. These insights can also be used by gueuze producers to better inform their customers about the quality of young and old gueuze beers.
Novel Alphaproteobacteria transcribe genes for nitric oxide transformation at high levels in a marine oxygen-deficient zone
Authors: Elbon Claire E. , Stewart Frank J. , Glass Jennifer B.
Published: March 2024

Marine oxygen-deficient zones (ODZs) are portions of the ocean where intense nitrogen loss occurs primarily via denitrification and anammox. Despite many decades of study, the identity of the microbes that catalyze nitrogen loss in ODZs is still being elucidated. Intriguingly, high transcription of genes in the same family as the nitric oxide dismutase (
nod
) gene from Methylomirabilota has been reported in the anoxic core of ODZs. Here, we show that the most abundantly transcribed
nod
genes in the Eastern Tropical North Pacific ODZ belong to a new order (UBA11136) of Alphaproteobacteria
,
rather than Methylomirabilota as previously assumed. Gammaproteobacteria and Planctomycetia also transcribe
nod
, but at lower relative abundance than UBA11136 in the upper ODZ. The
nod
-transcribing Alphaproteobacteria likely use formaldehyde and formate as a source of electrons for aerobic respiration, with additional electrons possibly from sulfide oxidation. They also transcribe multiheme cytochrome (here named
ptd
) genes for a putative porin-cytochrome protein complex of unknown function, potentially involved in extracellular electron transfer. Molecular oxygen for aerobic respiration may originate from nitric oxide dismutation via cryptic oxygen cycling. Our results implicate Alphaproteobacteria order UBA11136 as a significant player in marine nitrogen loss and highlight their potential in one-carbon, nitrogen, and sulfur metabolism in ODZs.

IMPORTANCE

In marine oxygen-deficient zones (ODZs), microbes transform bioavailable nitrogen to gaseous nitrogen, with nitric oxide as a key intermediate. The Eastern Tropical North Pacific contains the world’s largest ODZ, but the identity of the microbes transforming nitric oxide remains unknown. Here, we show that highly transcribed nitric oxide dismutase (
nod
) genes belong to Alphaproteobacteria of the novel order UBA11136, which lacks cultivated isolates. These Alphaproteobacteria show evidence for aerobic respiration, using oxygen potentially sourced from nitric oxide dismutase, and possess a novel porin-cytochrome protein complex with unknown function. Gammaproteobacteria and Planctomycetia transcribe
nod
at lower levels. Our results pinpoint the microbes mediating a key step in marine nitrogen loss and reveal an unexpected predicted metabolism for marine Alphaproteobacteria.
Halocin H4 is activated through cleavage by halolysin HlyR4
Authors: Chen Shaoxing , Dai Yongpei , Ke Juntao , Luo Yuqing , Wang Chuangming , Hao Yuling , Zhang Aodi , Han Jing , Xiang Hua
Published: March 2024

Halocins are antimicrobial peptides secreted by haloarchaea capable of inhibiting the growth of other haloarchaea or bacteria. Halocin H4 (HalH4) is secreted by the model halophilic archaeon
Haloferax mediterranei
ATCC 33500. Despite attempts to express
halH4
heterologously in
Escherichia coli
and subsequent careful renaturation procedures commonly employed for haloarchaeal proteins, no active halocin was obtained. However, it was discovered that the antihaloarchaeal activity of this halocin could be activated through cleavage by halolysin R4 (HlyR4), a serine protease also secreted by
Hfx. mediterranei
ATCC 33500. Replacement of the cysteine at the number 115 amino acid with glycine and deletion of the internal trans-membrane region (15 aa) markedly abolished HalH4’s antihaloarchaeal activity. Compared to the N-terminus, the C-terminal amino acid sequence was found to be more crucial for HalH4 to exert its antihaloarchaeal activity. Mass spectrometry analysis revealed that the biologically active antihaloarchaeal peptide produced after hydrolytic cleavage by HlyR4 was the C-terminus of HalH4, suggesting a potential mechanism of action involving pore formation within competitor species’ cell membranes. Taken together, this study offers novel insights into the interplay between halocins and secreted proteases, as well as their contribution to antagonistic interaction within haloarchaea.

IMPORTANCE

The antihaloarchaeal function of halocin H4 (HalH4) can be activated by extracellular proteases from haloarchaea, as demonstrated in this study. Notably, we report the first instance of halocin activation through proteolytic cleavage, highlighting its significance in the field. The C-terminus of HalH4 (CTH4) has been identified as the antihaloarchaeal peptide present in hydrolysates generated by HlyR4. The CTH4 exhibited inhibitory activity against a range of haloarchaeal species (
Haloarchaeobius
spp.,
Haloarcula
spp.,
Haloferax
spp.,
Halorubellus
spp., and
Halorubrum
spp.), as well as selected bacterial species (
Aliifodinibius
spp. and
Salicola
spp.), indicating its broad-spectrum inhibitory potential across domains. The encoding gene of halocin HalH4,
halH4
, from the model halophilic archaeon
Haloferax mediterranei
ATCC 33500 can be expressed in
Escherichia coli
without codon optimization.
Hopanoid lipids promote soybean
–Bradyrhizobium
symbiosis
Authors: Pan Huiqiao , Shim Ashley , Lubin Matthew B. , Belin Brittany J.
Published: March 2024

The symbioses between leguminous plants and nitrogen-fixing bacteria known as rhizobia are well known for promoting plant growth and sustainably increasing soil nitrogen. Recent evidence indicates that hopanoids, a family of steroid-like lipids, promote
Bradyrhizobium
symbioses with tropical legumes. To characterize hopanoids in
Bradyrhizobium
symbiosis with soybean, we validated a recently published cumate-inducible hopanoid mutant of
Bradyrhizobium
diazoefficiens USDA110, Pcu-
shc
::∆
shc
. GC-MS analysis showed that this strain does not produce hopanoids without cumate induction, and under this condition, is impaired in growth in rich medium and under osmotic, temperature, and pH stress.
In planta
, Pcu-
shc
::∆
shc
is an inefficient soybean symbiont with significantly lower rates of nitrogen fixation and low survival within the host tissue. RNA-seq revealed that hopanoid loss reduces the expression of flagellar motility and chemotaxis-related genes, further confirmed by swim plate assays, and enhances the expression of genes related to nitrogen metabolism and protein secretion. These results suggest that hopanoids provide a significant fitness advantage to
B. diazoefficiens
in legume hosts and provide a foundation for future mechanistic studies of hopanoid function in protein secretion and motility.

IMPORTANCE

A major problem for global sustainability is feeding our exponentially growing human population while available arable land decreases. Harnessing the power of plant-beneficial microbes is a potential solution, including increasing our reliance on the symbioses of leguminous plants and nitrogen-fixing rhizobia. This study examines the role of hopanoid lipids in the symbiosis between
Bradyrhizobium diazoefficiens
USDA110, an important commercial inoculant strain, and its economically significant host soybean. Our research extends our knowledge of the functions of bacterial lipids in symbiosis to an agricultural context, which may one day help improve the practical applications of plant-beneficial microbes in agriculture.
Whole-genome sequences of
Campylobacter coli
and
Campylobacter jejuni
isolates from rhesus macaques (
Macaca mulatta
) with and without intestinal disease
Authors: Bacon Rebecca L. , Norman Keri N. , Nickodem Colette A. , Vinasco Javier A. , Gray Stanton B. , Hodo Carolyn L. , Lawhon Sara D.
Published: March 2024

Campylobacter jejuni
or
Campylobacter coli
infection can lead to post-infectious irritable bowel syndrome in humans and may produce a similar syndrome in rhesus macaques (
Macaca mulatta
). We report the complete genomes of 8
C
.
jejuni
isolates and 103
C
.
coli
isolates obtained from rhesus macaques with and without intestinal disease.
Linking ecosystem multifunctionality to microbial community features in rivers along a latitudinal gradient
Authors: Cai Miaomiao , Zhang Caifang , Ndungu Caroline Njambi , Liu Guihua , Liu Wenzhi , Zhang Quanfa
Published: March 2024

Microorganisms regulate numerous ecosystem functions and show considerable differences along a latitudinal gradient. Although studies have revealed the latitudinal patterns of microbial community structure and single ecosystem function, the latitudinal patterns of ecosystem multifunctionality (EMF) and how microbial communities affect EMF along a latitudinal gradient remain unclear. Here, we collected channel sediments, riparian rhizosphere soils, and riparian bulk soils from 30 rivers across China and calculated EMF using 18 variables related to nitrogen cycling, nutrient pool, plant productivity, and water quality. We also determined microbial diversity (taxonomic and functional) and microbial network complexity using metagenomic sequencing. The results showed that EMF significantly decreased with increasing latitude in riparian rhizosphere and bulk soils but not in channel sediments. Microbial taxonomic and functional richness (observed species) in channel sediments were significantly higher in the low-latitude group than in the high-latitude group. However, microbial co-occurrence networks were more complex in the high-latitude group compared with the low-latitude group. Abiotic factors, primarily geographic and climatic factors, contributed more to EMF than microbial diversity and network complexity parameters in which only betweenness centralization had a significant relationship with EMF. Together, this study provides insight into the latitudinal pattern of EMF in rivers and highlights the importance of large-scale factors in explaining such latitudinal patterns.

IMPORTANCE

Ecosystem multifunctionality (EMF) is the capacity of an ecosystem to provide multiple functions simultaneously. Microorganisms, as dominant drivers of belowground processes, have a profound effect on ecosystem functions. Although studies have revealed the latitudinal patterns of microbial community structure and single ecosystem function, the latitudinal patterns of EMF and how microbial communities affect EMF along a latitudinal gradient remain unclear. We collected channel sediments, riparian rhizosphere soils, and riparian bulk soils from 30 rivers along a latitudinal gradient across China and calculated EMF using 18 variables related to nitrogen cycling, nutrient pool, plant productivity, and water quality. This study fills a critical knowledge gap regarding the latitudinal patterns and drivers of EMF in river ecosystems and gives new insights into how microbial diversity and network complexity affect EMF from a metagenomic perspective.
Evolutionary trends in antifungal resistance: a meta-analysis
Authors: Niu Xueke , Al-Hatmi Abdullah M. S. , Vitale Roxana G. , Lackner Michaela , Ahmed Sarah A. , Verweij Paul E. , Kang Yingqian , de Hoog Sybren
Published: March 2024

The present paper includes a meta-analysis of literature data on 318 species of fungi belonging to 34 orders in their response to 8 antifungal agents (amphotericin B, caspofungin, fluconazole, itraconazole, ketoconazole, posaconazole, terbinafine, and voriconazole). Main trends of MIC results at the ordinal level were visualized. European Committee on Antimicrobial Susceptibility Testing and Clinical & Laboratory Standards Institute (CLSI) clinical breakpoints were used as the staff gauge to evaluate MIC values ranging from resistance to susceptibility, which were subsequently compared with a phylogenetic tree of the fungal kingdom. Several orders (
Hypocreales, Microascales
, and
Mucorales
) invariably showed resistance. Also the basidiomycetous orders
Agaricales, Polyporales, Sporidiales, Tremellales
, and
Trichosporonales
showed relatively high degrees of azole multi-resistance, while elsewhere in the fungal kingdom, including orders with numerous pathogenic and opportunistic species, that is,
Onygenales, Chaetothyiales, Sordariales
, and
Malasseziales
, in general were susceptible to azoles. In most cases, resistance vs susceptibility was consistently associated with phylogenetic distance, members of the same order showing similar behavior.

IMPORTANCE

A kingdom-wide the largest set of published wild-type antifungal data comparison were analyzed. Trends in resistance in taxonomic groups (monophyletic clades) can be compared with the phylogeny of the fungal kingdom, eventual relationships between fungus–drug interaction and evolution can be described.
Multiscale structures of crust-mantle beneath the South China block and their geodynamic implication
Authors: Cheng Siyuan , Shen Xuzhang , Dong Shuwen , Gao Rui , Cui Jianjun , Huang He , Li Minjuan , Shao Ruotong
Published: March 2024

The South China block is an ideal location in which to study the impact of paleo-Pacific plate subduction on the upper mantle and crustal structures of the overriding plate, as well as the mechanism of lithospheric thinning. By integrating data from permanent seismic stations of the China Seismic Network and a dense seismic array at Xuefeng Mountain, this study employed P- and S-wave receiver functions (RFs) to image multiscale structures of crust-mantle across the South China block, thereby providing constraints for a comprehensive understanding of its tectonic evolution. The main findings are as follows: (1) The thickness of lithosphere and crust gradually decreases from northwest (NW) to southeast (SE). (2) Beneath the Xuefeng Mountain uplift zone, the P-to-S conversion from the 660 km discontinuity arrives earlier than that predicted from a one-dimensional model, other weak discontinuities can be traced in the upper mantle, including the lithosphere-asthenosphere boundary, the crust becomes thinner, and the Conrad discontinuity becomes deeper. Referring to previous results from tomography and geological reconstructions, we deduce that lithospheric delamination might have occurred beneath the Xuefeng Mountain uplift zone, and the delaminated lithosphere penetrated the upper mantle and reached the mantle transition zone.
Protocol for venoarterial ExtraCorporeal Membrane Oxygenation to reduce morbidity and mortality following bilateral lung TransPlantation: the ECMOToP randomised controlled trial
Authors: Messika Jonathan , Eloy Philippine , Boulate David , Charvet Aude , Fessler Julien , Jougon Jacques , Lacoste Philippe , Mercier Olaf , Portran Philippe , Roze Hadrien , Sage Edouard , Thes Jacques , Tronc Francois , Vourc'h Mickael , Montravers Philippe , Castier Yves , Mal Herve , Mordant Pierre
Published: March 2024

Introduction

Lung transplantation (LTx) aims at improving survival and quality of life for patients with end-stage lung diseases. Venoarterial extracorporeal membrane oxygenation (VA-ECMO) is used as intraoperative support for LTx, despite no precise guidelines for its initiation. We aim to evaluate two strategies of VA-ECMO initiation in the perioperative period in patients with obstructive or restrictive lung disease requiring bilateral LTx. In the control ‘on-demand’ arm, high haemodynamic and respiratory needs will dictate VA-ECMO initiation; in the experimental ‘systematic’ arm, VA-ECMO will be pre-emptively initiated. We hypothesise a ‘systematic’ strategy will increase the number of ventilatory-free days at day 28.

Methods and analysis

We designed a multicentre randomised controlled trial in parallel groups. Adult patients with obstructive or restrictive lung disease requiring bilateral LTx, without a formal indication for pre-emptive VA-ECMO before LTx, will be included. Patients with preoperative pulmonary hypertension with haemodynamic collapse, ECMO as a bridge to transplantation, severe hypoxaemia or hypercarbia will be secondarily excluded. In the systematic group, VA-ECMO will be systematically implanted before the first pulmonary artery cross-clamp. In the on-demand group, VA-ECMO will be implanted intraoperatively if haemodynamic or respiratory indices meet preplanned criteria. Non-inclusion, secondary exclusion and VA-ECMO initiation criteria were validated by a Delphi process among investigators. Postoperative weaning of ECMO and mechanical ventilation will be managed according to best practice guidelines. The number of ventilator-free days at 28 days (primary endpoint) will be compared between the two groups in the intention-to-treat population. Secondary endpoints encompass organ failure occurrence, day 28, day 90 and year 1 vital status, and adverse events.

Ethics and dissemination

The sponsor is the Assistance Publique–Hôpitaux de Paris. The ECMOToP protocol version 2.1 was approved by Comité de Protection des Personnes Ile de France VIII. Results will be published in international peer-reviewed medical journals.

Trial registration number

NCT05664204.