bluuebunny/crossref_metadata_2025 huggingface dataset:
Advancing Aquaculture Sustainability: A Comprehensive Review of Biofloc Technology Trends, Innovative Research Approaches, and Future Prospects
Authors: Liu Gang , Verdegem Marc , Ye Zhangying , Zhao Jian , Xiao Jinxing , Liu Xingguo , Liang Qinlang , Xiang Kun , Zhu Songming
Published: September 2024

Biofloc technology (BFT), initially adapted for shrimp farming in the 1970s, represents a sophisticated ecosystem of microorganisms designed to enhance aquaculture productivity and sustainability. Despite its established history, research into BFT is surprisingly still at an early stage globally. This review conducted a bibliometric analysis of 612 articles from major aquaculture journals spanning 2008–2023 to systematically explore the development, trends, and focal points of BFT research. The analysis revealed that the bulk of significant contributions originates from Brazil and China, and highlighting areas of interest can be categorized into four hotspots, such as (1) efficient nitrogen transformation, (2) biofloc microbiology, (3) biofloc's immunostimulant properties, and (4) the evaluation of research methodologies. At the end, the microecology concept was introduced, and the cross‐discipline methods were promoted in the aquaculture field. Notably, much of the BFT research is still at an exploratory phase, with numerous functional bacteria unidentified and optimization strategies for BFT underdeveloped. These gaps present opportunities for enhancing aquaculture through improvements in wastewater management, product quality, safety, and yield. Furthermore, the review notes a growing trend in applying microbiome research and microecological analysis in aquaculture, with high‐throughput sequencing data increasingly used to understand microbial interactions and nitrogen transformation within bioflocs. This direction promises to unlock further insights into the complex microbial ecosystems of bioflocs and their applications in sustainable aquaculture.
No signs of mast cell involvement in long‐COVID: A case–control study
Authors: Lenning Ole Bernt , Jonsson Grete , Grimstad Tore , Janssen Emiel A. M. , Braut Geir Sverre , Berven Frode , Omdal Roald
Published: September 2024

Long‐COVID caused by SARS‐CoV‐2 infection has significant and increasing effects on human health worldwide. Although a unifying molecular or biological explanation is lacking, several pathophysiological mechanisms have been proposed. Involvement of mast cells—evolutionary old “multipurpose” innate immune cells—was reported recently in studies of acute infection and post‐acute‐COVID‐19 syndrome. Mast cell activity has been suggested in long‐COVID. In this case–control study, we compared data from 24 individuals with long‐COVID (according to the NICE criteria) and 24 age‐ and sex‐matched healthy individuals with a history of SARS‐CoV‐2 infection without developing sequelae. Serum levels of the proteases beta‐tryptase (TPSB2) and carboxypeptidase (CPA3), which are mast cell specific, were measured using immunoassays. The values were compared between the two groups and correlated to measures of physical exertional intolerance. TPSB2 and CPA3 levels were median (range) 26.9 (2.0–1000) and 5.8 (1.5–14.0) ng/mL, respectively, in the long‐COVID group. The corresponding values in the control group were 10.9 (2.0–1000) (p = 0.93) and 5.3 (3.5–12.9) ng/mL (p = 0.82). No significant correlations between TPSB2 or CPA3 levels and scores on the ten physical subscales of SF‐36, 3.1–3.10 were revealed. We found no significant differences in the levels of mast cell activation markers TPSB2 and CPA3 between the long‐COVID and control groups and no correlations with proxy markers of exercise intolerance. Mast cell activation does not appear to be part of long‐term pathogenesis of long‐COVID, at least in the majority of patients.
On the experience of goals: Differentiating goal‐generic value from goal‐specific value
Authors: Converse Benjamin A. , Roberts Annabelle R. , Hennecke Marie , Fishbach Ayelet
Published: September 2024

We distinguish between goal‐specific value, which refers to the intrinsic and extrinsic benefits associated with a particular goal (“value derived from the goal”), and goal‐generic value, which refers to the benefits associated with having, pursuing, or completing a goal in general (“value derived from a goal”). Motivation theory and research have traditionally, if tacitly, sought to explain decision‐making (e.g., What to prioritize? How much to invest?) based on goal‐specific value. But several goal‐related decision regularities are not easily explained by accounting for goal‐specific value alone, such as online workers choosing a lower‐paying assignment (over a higher‐paying assignment) if it allows them to complete the last step in a sequence and college students electing to do more work sooner (rather than less work later) if it provides them closure. Accounting for goal‐generic value—such as the positive experiences of purpose, progress, closure, and accomplishment—offers additional insight into people's decisions. More generally, auditing goals in a way that accounts for both goal‐specific value and goal‐generic value is crucial for understanding goal pursuits.
Fostering students' inquiry aptitudes and collaborative reasoning in higher education science courses with social annotation tools and collaborative platforms
Authors: Elmi Chiara
Published: September 2024

Interactive digital technologies are playing an increasingly important part in education for enhancing collaborative learning processes and improving engagement. Social annotation (SA) tools and collaborative platforms are an innovative way to involve students to give and take feedback, annotate, and brainstorm on complex topics in science, technology, engineering, and mathematics (STEM). This article focuses on innovative practices that integrate inquiry‐based discussions using SA tools and collaborative platforms to promote undergraduate students' interest and curiosity about sciences. In this article, lectures were combined with inquiry‐based discussions using an open education SA tool and an open‐access collaborative platform to engage students in a meaningful dialog with peers on scientific topics. Students debated with peers on scientific content in an online environment. Findings show that the integration of inquiry‐based discussions using SA tools and collaborative platforms provides a practical way to effectively improve students interest in science. The information reported in this article can support STEM instructors in designing collaborative learning activities in online and hybrid settings that spark students' curiosity and inquiry attitude about natural sciences.
An advanced learning approach for detecting sarcasm in social media posts: Theory and solutions
Authors: Roy Pradeep Kumar
Published: September 2024

Objective

Users of social media platforms such as Facebook, Instagram, and Twitter can view and share their daily life events through text, photographs, or videos. These platforms receive many sarcastic posts daily because there were fewer limits on what could be posted. The presence of multiple languages and media types in a single post makes it harder to identify sarcastic messages on the current platform than on posts written solely in English.

Methods

This study provides both the theory and solutions about sarcastic post detection on social platforms. Hindi–English code‐mixed data were used to train and test the automated models for sarcasm detection. The models in this study were constructed using traditional machine learning, deep neural networks, LSTM (long short‐term memory), CNN (convolutional neural network), and the combinations of BERT (Bidirectional Encoder Representations from Transformers) with LSTM.

Results

The experimental results confirm that in the Hindi–English code‐mixed data set, the CNN, LSTM, and BERT‐LSTM ensemble perform best for sarcasm detection. The proposed model achieved an accuracy of 96.29 percent and outperformed by 2.29 percent compared to the existing models.

Conclusion

The performance of the proposed system strengthens the code‐mixed sarcastic post detection on social platforms. The model will help filter not only English but also Hindi‐English code‐mixed sarcastic posts on social platforms.
Domains of baseless belief and the characteristics of believers
Authors: Roscoe Douglas D. , Shapiro Amy M. , Ayotte Brian
Published: September 2024

Objective

An extensive literature examines the prevalence of conspiracy theories and the factors that determine why some people believe them. Conspiracy theories are only one example of baseless beliefs, which we define as beliefs that are not epistemically warranted by the available evidence. The goals of this research were to determine if there are discrete domains of baseless beliefs and to identify the psychological and cognitive factors most closely associated with each type.

Methods

We surveyed 435 U.S. adults about their baseless beliefs and measured an extensive set of cognitive, epistemological, and personal characteristics.

Results

Four distinct domains of baseless belief were discovered, which we label conservative controversies, classic coverups, magical thoughts, and pseudoscience. The data suggest the confidence people have in these beliefs differs across domains and reveal clear differences in the cognitive, epistemological, and personality factors predicting belief in each domain.

Conclusion

Baseless beliefs encompass a number of distinct domains, and the psychological dynamics underlying belief acquisition vary across these domains. This finding suggests caution in generalizing from studies examining only one domain. The prominent role of conservatism documented in the literature on conspiracy theories, for example, is weaker or not present at all in other domains.
Phosphorus acquisition by faba bean, blue lupin, and chickpea in relation to soil phosphorus status
Authors: Gotz Lenir Fátima , Pavinato Paulo Sergio , Condron Leo Murtagh
Published: September 2024

The efficiency of soil phosphorus (P) mobilization and uptake by plants depends on a complex combination of factors, including plant P acquisition strategies and soil P availability. The objective of this study was to assess and compare the capabilities of three legume species (blue lupin (Lupinus angustifolius L.), faba bean (Vicia faba L.), and chickpea (Cicer arietinum L.)), which may be used as green manures in temperate crop systems to acquire P from a soil with different levels of plant‐available P. Three cycles of each legume were grown in a glasshouse over a 6 month period in the same soil type with high (Olsen P: 47 mg kg−1) and low (Olsen P: 9 mg kg−1) levels of plant‐available P. Measurements included above—and below—ground plant biomass and P uptake, in addition to determination of acid and alkaline phosphomonoesterase activities, microbial P, and P fractions in soil at the end of the experiment. In both soils, plant biomass, P uptake, and microbial P were all higher under faba bean compared to blue lupin and chickpea (p < .05). In the low‐P soil, faba bean increased alkaline phosphomonoesterase activity (p < .05). Significant depletion of inorganic P in the soluble (46%–69%), labile (29%–42%), and moderately labile (15%–16%) pools and increase of organic P in the labile (13%–18%) and total (7%–13%) pools occurred under faba bean compared with blue lupin, while changes under chickpea were between those determined for faba bean and blue lupin (p < .05). The findings of this study indicated that inclusion of faba bean green manure may have the potential to improve overall P use efficiency by enhancing mobilization of labile soil inorganic P, although further research is required to investigate mobilization of more stable forms of soil legacy P and quantify the potential of faba bean as a green manure crop under field conditions.
PyGRF: An Improved Python Geographical Random Forest Model and Case Studies in Public Health and Natural Disasters
Authors: Sun Kai , Zhou Ryan Zhenqi , Kim Jiyeon , Hu Yingjie
Published: September 2024

Geographical random forest (GRF) is a recently developed and spatially explicit machine learning model. With the ability to provide more accurate predictions and local interpretations, GRF has already been used in many studies. The current GRF model, however, has limitations in its determination of the local model weight and bandwidth hyperparameters, potentially insufficient numbers of local training samples, and sometimes high local prediction errors. Also, implemented as an R package, GRF currently does not have a Python version which limits its adoption among machine learning practitioners who prefer Python. This work addresses these limitations by introducing theory‐informed hyperparameter determination, local training sample expansion, and spatially weighted local prediction. We also develop a Python‐based GRF model and package, PyGRF, to facilitate the use of the model. We evaluate the performance of PyGRF on an example dataset and further demonstrate its use in two case studies in public health and natural disasters.
Survey of ocular abnormalities in a population of Turkmen horses
Authors: Faghihi Houman , Gharibi Afsaneh , Ansari Mood Maneli , Rajaei Seyed Mehdi , Alavi Seyyed Morteza
Published: September 2024

Objective

The aim of this study was to detect and describe ocular abnormalities in a population of Turkmen horses.

Animals Studied

A total of 55 Turkmen horses (33 mares and 22 stallions) from one herd were evaluated in this study.

Procedure(s)

Demographic data (Age, Sex, Coat color) were recorded. All animals underwent complete ophthalmic examination. The Schirmer tear test ‐I (STT‐I) was performed for all horses prior to other diagnostic tests. Neuro‐ophthalmic examinations (menace response, dazzle reflex, pupillary light reflex, maze test, and visual tracking) were carried out in different lighting situations (bright and dim lights). Slit lamp biomicroscopy, direct and indirect ophthalmoscopy, fluorescein staining, and tonometry were performed for each horse.

Results

The mean (standard deviation) age of horses was 5.7 (4.6) years (range of 1–17 years). In total, 18 horses (32.7%) had ocular‐related lesions. Cataract, iris hyperpigmentation and corneal edema were the most identified conditions in the horses of this study.

Conclusions

About one‐third of studied horses had at least one ocular abnormality. No ocular abnormalities attributed to the distinct cream/gold coat color were identified, which the Turkmen horse is known for.
Delimiting species boundaries within the Babyloniidae (Mollusca: Gastropoda: Neogastropoda) using multi‐locus phylogenetic analysis
Authors: Yen Yu‐Hsiu , Joseph Julian , Liu Shang‐Yin Vanson
Published: September 2024

The Babyloniidae is a family of marine snails consisting of 21 species and two genera. Current taxonomic debates on the Babyloniidae are mainly due to their extremely similar shell morphologies, which have led to incorrect locality records and mislabelling in legal or illegal international trade. We have therefore constructed a phylogeny of the Babyloniidae with high species coverage (57% of the family) by using multi‐locus genes (cytochrome c oxidase subunit I [COI], 16S, and H3) with four species delimitation methods (Best Close Match [BCM], Assemble Species by Automatic Partitioning [ASAP], Bayesian Poisson Tree Process [bPTP] and Multi‐rate Poisson Tree Processes [mPTP]). Based on our results, 13 clades/operational taxonomic unit were observed, which confirms pre‐existing species status for 10 Babylonia and one Zemiropsis taxa: B. areolata (Link, 1807), B. borneensis (Sowerby II, 1864), B. feicheni Shikama, 1973, B. formosae (Sowerby II, 1866), B. japonica (Reeve, 1842), B. lutosa (Lamarck, 1816), B. pieroangelai Cossignani, 2008, B. spirata (Linnaeus, 1758), B. valentiana (Swainson, 1822), B. zeylanica (Bruguière, 1789) and Z. papillaris (Sowerby I, 1825). A monophyletic group with four species collected from Indonesia which includes B. spirata f. balinensis Cossignani, 2009, B. spirata f. semipicta (Sowerby II, 1866) and B. angusta Altena & Gittenberger, 1981, implying they should belong to a single species, B. semipicta. Additionally, we suggest B. formosae habei Altena & Gittenberger, 1981 should be escalated as B. habei, and not as a subspecies.
Equidistribution of expanding degenerate manifolds in the space of lattices
Authors: Shah Nimish A. , Yang Pengyu
Published: September 2024

For the space of unimodular lattices in a Euclidean space, we give necessary and sufficient conditions for equidistribution of expanding translates of any real‐analytic submanifold under a diagonal flow. This work extends the earlier result of Shah in the case of nondegenerate submanifolds. We apply the above dynamical result to show that if the affine span of a real‐analytic submanifold in a Euclidean space satisfies certain Diophantine and arithmetic conditions, then almost every point on the manifold is not Dirichlet‐improvable.
Singularities of secant varieties from a Hodge theoretic perspective
Authors: Olano Sebastián , Raychaudhury Debaditya , Song Lei
Published: September 2024

We study the singularities of secant varieties of smooth projective varieties using methods from birational geometry when the embedding line bundle is sufficiently positive. More precisely, we study the Du Bois complex of secant varieties and its relationship with the sheaves of differential forms. Through this analysis, we give a necessary and sufficient condition for these varieties to have ‐Du Bois singularities (in a sense that was proposed in Shen, Venkatesh, and Vo [On k‐Du Bois and k‐rational singularities, arXiv e‐prints (June 2023), arXiv:2306.03977]). In addition, we show that the singularities of these varieties are never higher rational, by giving a classification of the cases when they are pre‐1‐rational. From these results, we deduce several consequences, including a Kodaira–Akizuki–Nakano type vanishing result for the reflexive differential forms of the secant varieties.
Return on investment of tobacco control measures: a systematic review protocol
Authors: Bhattacharya Paramita , Khatoon Sajda , Roy Suraya , Mukherjee Nirmalya , Yadav Amit , Lal Pranay , Pokhrel Subhash , John Denny
Published: September 2024

Objective:

The objective of this systematic review will be to estimate the return on investment (ROI) and social return on investment (SROI) on tobacco control measures.

Introduction:

Tobacco consumption has been proven to be associated with a huge epidemiological, humanistic, and economic burden. National and international organizations are making concerted efforts to control tobacco use. However, currently, there are no conclusive estimates of the ROI and SROI of such programs and policies.

Inclusion criteria:

This review will include all studies that evaluate the ROI or SROI on tobacco control programs and policies on tobacco users and probable tobacco users globally.

Methods:

This review will follow the JBI methodology for systematic reviews of economic evidence. Databases to be searched will include Embase (Ovid), MEDLINE (PubMed), Cochrane Central Register of Controlled Trials (CENTRAL), Health Economic Evaluation Database (HEED), National Health Service Economic Evaluation Database (NHS EED), CEA Registry, LILACS, Science Direct, Web of Science, EconLit, and Google Advanced Search. Gray literature will also be searched for in non-academic databases, including the websites of various civil societies and non-governmental organizations involved in tobacco control. Two independent reviewers will screen titles/abstracts, and later full-text studies. Critical appraisal will be conducted using the JBI checklist for economic evaluations and the SROI Quality Framework. Data will be extracted and synthesized using JBI data extraction forms and synthesis tools. The MPOWER framework will be considered for data synthesis across all selected studies using narrative synthesis, tables, and figures.

Systematic review registration number:

PROSPERO CRD42023391591
THE THERAPEUTIC POTENTIAL OF PRECONDITIONED MESENCHYMAL STEM CELLS IN ATHEROSCLEROSIS
Authors: Sekenova A.Ye. , Ogay V.B.
Published: September 2024

Atherosclerosis (AS) is a multifactorial and inflammatory disease the cause of which is the formation of lipid and cholesterol plaques on the inner wall of blood vessels. Experimental and clinical studies have shown that the pathogenesis of atherosclerosis is, in particular, connected with inflammatory reactions. Recent studies reported that preconditioned mesenchymal stem cells (MSCs) possess an enhanced immunomodulatory potential. The purpose of the study was to investigate the therapeutic potential of preconditioned MSCs in the development of atherosclerosis.
MSCs were isolated from the compact bone of mice by standard protocol. The characterization was conducted using flow cytometry, CFU assay and three-lineage differentiation. Cells were preconditioned with different combinations of cytokines and the optimal concentrations were determined by ELISA and by analysis of co-culturing with lymphocytes. The cytokine-preconditioned MSCs were administrated to  mice with induced atherosclerosis. The lipids analysis, measuring of mouse spleens’ weights, ELISA and histological analysis of the aorta sections were done after 8-th weeks.
We isolated MSCs and then confirmed the possession of the immunomodulatory properties. Preconditioning with the TNF-α cytokine effectively increased the immunomodulatory properties of MSCs compared to untreated MSCs in vitro. The results of in vivo study that the use of TNF-α-preconditioned MSCs reduced the development of atherosclerosis in  mice compared to untreated MSCs: it increased the level of Treg cells in the spleen of mice; significantly reduced the levels of TNF-α and IFN-γ in blood serum; significantly reduced the spleen weights of mice; slightly decreased the total cholesterol levels and also increased HDL levels. Administration of TNF-α-preconditioned MSCs reduced the size of atherosclerotic plaques in the aorta of  mice.
The results of this study demonstrated the effect of cytokine-preconditioned MSCs in the inhibition of the development of atherosclerosis in a mouse model. However, for application as a therapy for suffered patients additional studies are needed. Besides, using of TNF-α preconditioned MSCs can be considered in other preclinical studies of the different diseases.
Mechanical Properties Inside Origami-Inspired Structures: An Overview
Authors: Yan Peng , Huang Hailin , Meloni Marco , Li Bing , Cai Jianguo
Published: September 2024

In recent decades, origami has transitioned from a traditional art form into a systematic field of scientific inquiry, characterized by attributes such as high foldability, lightweight frameworks, diverse deformation modes, and limited degrees-of-freedom. Despite the abundant literature on smart materials, actuation methods, design principles, and manufacturing techniques, comprehensive reviews focusing on the mechanical properties of origami-inspired structures are relatively rare and unsystematic. This review aims to fill this void by analyzing and summarizing the significant studies conducted on the mechanical properties of origami-inspired structures from 2013 to 2023. We begin with an overview that includes essential definitions of origami, classical origami patterns, and their associated tessellated or stacked structures. Following this, we delve into the principal dynamic modeling method for origami and conduct an in-depth analysis of the key mechanical properties of origami-inspired structures. These properties include tunable stiffness, bistability and multistability, metamechanical properties demonstrated by origami-based metamaterials, and bio-inspired mechanical properties. Finally, we conclude with a comprehensive summary that discusses the current challenges and future directions in the field of origami-inspired structures. Our review provides a thorough synthesis of both the mechanical properties and practical applications of origami-inspired structures, aiming to serve as a reference and stimulate further research.
Beyond the Esports Horizon in Sport Psychology: An Introduction to the Special Issue
Authors: Price David , Swettenham Laura
Published: September 2024

Welcome to this special issue in Case Studies in Sport and Exercise Psychology, which focuses on the applied sport psychology practice landscape, within the world of esports. In this prologue, we aim to provide a contextual backdrop regarding the unprecedented growth of esports, elucidate the current status quo of sport psychology practice in the world of esports, and highlight the growing call for case studies to bridge the research–practice gap to better inform practitioners operating in esports. In this prologue, we also provide brief commentaries on the four case studies contained in this special issue, to give readers an insight on what to expect. Finally, in this special issue, we offer an epilogue that shares key reflections from the four case studies, as well as future research and practice opportunities in the exciting world of esports.
Operationalizing General Mechanical Skill in Time-Pressure Action Esports
Authors: Kim Jonghyun , Dunkel William , Lee Byungjoo
Published: September 2024

In time-pressure action esports games, a player’s mechanical skill refers to the ability to quickly and accurately control input devices such as a keyboard or mouse. In this study, we present a novel methodology to quantify and operationalize mechanical skills commonly required in game titles played with the same set of input devices (i.e., general mechanical skill). From this, differences in mechanical skills between players can be compared on a standard basis, regardless of game title, which offers new possibilities for esports talent development. As a result of partial least squares path modeling based on data from 292 players of four different game titles played with keyboard and mouse, we show that general mechanical skill is a valid construct and that it accounts for approximately 21% of the variance in players’ in-game achievement (or rank). To maximize impact, our software is released to the public, enabling anyone to operationalize general mechanical skills in time-pressure action esports games played with keyboard and mouse.
Maximally precise combinations to overcome metallo-β-lactamase-producing
Klebsiella pneumoniae
Authors: Kaur Jan Naseer , Klem Jack F. , Liu Yang , Boissonneault Katie Rose , Holden Patricia N. , Kreiswirth Barry , Chen Liang , Smith Nicholas M. , Tsuji Brian T.
Published: September 2024

Gram-negatives harboring metallo-β-lactamases (MBLs) and extended-spectrum β-lactamases (ESBLs) pose a substantial risk to the public health landscape. In ongoing efforts to combat these “superbugs,” we explored the clinical combination of aztreonam and ceftazidime/avibactam together with varying dosages of polymyxin B and imipenem against
Klebsiella pneumoniae
(
Kp
CDC Nevada) in a 9-day hollow fiber infection model (HFIM). As previously reported by our group, although the base of aztreonam and ceftazidime/avibactam alone leads to 3.34 log
10
fold reductions within 72 hours, addition of polymyxin B or imipenem to the base regimen caused maximal killing of 7.55 log
10
and 7.4 log
10
fold reduction, respectively, by the 72-hour time point. Although low-dose polymyxin B and imipenem enhanced the bactericidal activity as an adjuvant to aztreonam +ceftazidime/avibactam, regrowth to ~9 log
10
CFU/mL by 216 hours rendered these combinations ineffective. When aztreonam +ceftazidime/avibactam was supplemented with high-dose polymyxin B and or low-dose polymyxin B + imipenem, it resulted in effective long-term clearance of the bacterial population. Time lapse microscopy profiled the emergence of long filamentous cells in response to PBP3 binding due to aztreonam and ceftazidime. The emergence of spheroplasts via imipenem and damage to the outer membrane via polymyxin B was visualized as a mechanism of persister killing. Despite intrinsic
mgrB
and
bla
NDM-1
resistance, polymyxin B and β-lactam combinations represent a promising strategy. Future studies using an integrated molecularly precise pharmacodynamic approach are warranted to unravel the mechanistic details to propose optimal antibiotic combinations to combat untreatable, pan-drug-resistant Gram-negatives.
Anaerobic benzene oxidation in
Geotalea daltonii
involves activation by methylation and is regulated by the transition state regulator AbrB
Authors: Bullows James E. , Kanak Alison , Shedrick Lawrence , Kiessling Christina , Aklujkar Muktak , Kostka Joel , Chin Kuk-Jeong
Published: September 2024

Benzene is a widespread groundwater contaminant that persists under anoxic conditions. The aim of this study was to more accurately investigate anaerobic microbial degradation pathways to predict benzene fate and transport. Preliminary genomic analysis of
Geotalea daltonii
strain FRC-32, isolated from contaminated groundwater, revealed the presence of putative aromatic-degrading genes.
G. daltonii
was subsequently shown to conserve energy for growth on benzene as the sole electron donor and fumarate or nitrate as the electron acceptor. The
hbs
gene, encoding for 3-hydroxybenzylsuccinate synthase (Hbs), a homolog of the radical-forming, toluene-activating benzylsuccinate synthase (Bss), was upregulated during benzene oxidation in
G. daltonii
, while the
bss
gene was upregulated during toluene oxidation. Addition of benzene to the
G. daltonii
whole-cell lysate resulted in toluene formation, indicating that methylation of benzene was occurring. Complementation of σ
54
-
(deficient)
E. coli
transformed with the
bss
operon restored its ability to grow in the presence of toluene, revealing
bss
to be regulated by σ
54
. Binding sites for σ
70
and the transition state regulator AbrB were identified in the promoter region of the σ
54
-encoding gene
rpoN,
and binding was confirmed. Induced expression of
abrB
during benzene and toluene degradation caused
G. daltonii
cultures to transition to the death phase. Our results suggested that
G. daltonii
can anaerobically oxidize benzene by methylation, which is regulated by σ
54
and AbrB. Our findings further indicated that the benzene, toluene, and benzoate degradation pathways converge into a single metabolic pathway, representing a uniquely efficient approach to anaerobic aromatic degradation in
G. daltonii
.

IMPORTANCE

The contamination of anaerobic subsurface environments including groundwater with toxic aromatic hydrocarbons, specifically benzene, toluene, ethylbenzene, and xylene, has become a global issue. Subsurface groundwater is largely anoxic, and further study is needed to understand the natural attenuation of these compounds. This study elucidated a metabolic pathway utilized by the bacterium
Geotalea daltonii
capable of anaerobically degrading the recalcitrant molecule benzene using a unique activation mechanism involving methylation. The identification of aromatic-degrading genes and AbrB as a regulator of the anaerobic benzene and toluene degradation pathways provides insights into the mechanisms employed by
G. daltonii
to modulate metabolic pathways as necessary to thrive in anoxic contaminated groundwater. Our findings contribute to the understanding of novel anaerobic benzene degradation pathways that could potentially be harnessed to develop improved strategies for bioremediation of groundwater contaminants.
Molecular insights into the hydrolysis and transglycosylation of a deep-sea
Planctomycetota
-derived GH16 family laminarinase
Authors: Li Wei , Lin Shanshan , Wang Xianjie , Chen Shiting , Long Lijuan , Yang Jian
Published: September 2024

The biochemical and structural characteristics of
Pt
Lam, a laminarinase from deep-sea
Planctomycetota
, have been extensively elucidated, unveiling the fundamental molecular mechanisms governing substrate recognition and enzymatic catalysis.
Pt
Lam functions as an exo-laminarinase with the ability to sequentially hydrolyze laminarin, cleaving glucose units individually. Notably,
Pt
Lam exhibits proficient transglycosylation capabilities, utilizing various sugar alcohols as acceptors, with lyxose, in particular, yielding exclusively transglycosylated products. Structural analysis of both apo-
Pt
Lam and its laminarin oligosaccharide-bound complex revealed significant conformational alterations in active residues upon substrate binding. Moreover, pivotal residues involved in substrate recognition were identified, with subsequent mutation assays indicating the contribution of positive subsites in modulating exo-hydrolysis and transglycosidic activities. These results enhance our comprehension of laminarin cycling mechanisms by marine
Planctomycetota
, while also providing essential enzyme components for laminarin hetero-oligosaccharide synthesis.

IMPORTANCE

The ubiquitous
Planctomycetota
, with distinctive physiological traits, exert a significant influence on global carbon and nitrogen fluxes. Their intimate association with algae suggests a propensity for efficient polysaccharide degradation; however, research on glycoside hydrolases derived from
Planctomycetota
remains scarce. Herein, we unveil the GH16 family laminarinase
Pt
Lam from deep-sea
Planctomycetota
, shedding light on its catalytic mechanisms underlying hydrolysis and transglycosylation. Our findings elucidate the enzymatic pathways governing the marine laminarin cycle orchestrated by
Planctomycetota,
thereby fostering the exploration of novel polysaccharide hydrolases with promising practical implications.
Application and antagonistic mechanisms of atoxigenic
Aspergillus
strains for the management of fungal plant diseases
Authors: Wang Suyan , Wang Yanxia , Shi Xinchi , Herrera-Balandrano Daniela D. , Chen Xin , Liu Fengquan , Laborda Pedro
Published: September 2024

This review covers, for the first time, all methods based on the use of
Aspergillus
strains as biocontrol agents for the management of plant diseases caused by fungi and oomycetes. Atoxigenic
Aspergillus
strains have been screened in a variety of hosts, such as peanuts, maize kernels, and legumes, during the preharvest and postharvest stages. These strains have been screened against a wide range of pathogens, such as
Fusarium
,
Phytophthora
, and
Pythium
species, suggesting a broad applicability spectrum. The highest efficacies were generally observed when using non-toxigenic
Aspergillus
strains for the management of mycotoxin-producing
Aspergillus
strains. The modes of action included the synthesis of antifungal metabolites, such as kojic acid and volatile organic compounds (VOCs), secretion of hydrolytic enzymes, competition for space and nutrients, and induction of disease resistance.
Aspergillus
strains degraded
Sclerotinia sclerotiorum
sclerotia, showing high control efficacy against this pathogen. Collectively, although two
Aspergillus
strains have been commercialized for aflatoxin degradation, a new application of
Aspergillus
strains is emerging and needs to be optimized.
Infections caused by
Haemophilus ducreyi:
one organism, two stories
Authors: Al-Tawfiq Jaffar A. , Spinola Stanley M.
Published: September 2024

Chancroid, a sexually transmitted infection caused by
Haemophilus ducreyi
, is characterized by painful genital ulcers (GU) and inguinal lymphadenitis.
H. ducreyi
was recently described as a major cause of non-sexually transmitted cutaneous ulcers (CU) on the lower legs in children in yaws-endemic regions. This review explores the relationship between CU and GU strains of
H. ducreyi
; their clinical presentation, diagnosis, epidemiology, and treatment; and how findings from a human challenge model relate to GU and CU. We contrast the decline of GU with the persistence of CU caused by
H. ducreyi
. Factors such as transmission dynamics, control, and elimination efforts are discussed. Syndromic management and targeted treatment of sex workers can eradicate chancroid, while skin colonization by CU strains and environmental factors may necessitate topical treatments or vaccination for CU eradication. Efforts should focus on identifying additional reservoirs of CU strains, improving hygiene, and eliminating asymptomatic colonization to eradicate this painful infection in children.
Palmitoylation of SARS-CoV-2 Envelope protein is central to virus particle formation
Authors: Wang Zhaohuan , Qiu Manman , Ji Yue , Chai Keli , Liu Chenxi , Xu Fengwen , Guo Fei , Tan Juan , Liu Ruikang , Qiao Wentao
Published: September 2024

The Envelope (E) protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an integral structural protein in the virus particles. However, its role in the assembly of virions and the underlying molecular mechanisms are yet to be elucidated, including whether the function of E protein is regulated by post-translational modifications. In the present study, we report that SARS-CoV-2 E protein is palmitoylated at C40, C43, and C44 by palmitoyltransferases zDHHC3, 6, 12, 15, and 20. Mutating these three cysteines to serines (C40/43/44S) reduced the stability of E protein, decreased the interaction of E with structural proteins Spike, Membrane, and Nucleocapsid, and thereby inhibited the production of virus-like particles (VLPs) and VLP-mediated luciferase transcriptional delivery. Specifically, the C40/43/44S mutation of E protein reduced the density of VLPs. Collectively, these results demonstrate that palmitoylation of E protein is vital for its function in the assembly of SARS-CoV-2 particles.

IMPORTANCE

In this study, we systematically examined the biochemistry of palmitoylation of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) E protein and demonstrated that palmitoylation of SARS-CoV-2 E protein is required for virus-like particle (VLP) production and maintaining normal particle density. These results suggest that palmitoylated E protein is central for proper morphogenesis of SARS-CoV-2 VLPs in densities required for viral infectivity. This study presents a significant advancement in the understanding of how palmitoylation of viral proteins is vital for assembling SARS-CoV-2 particles and supports that palmitoyl acyltransferases can be potential therapeutic targets for the development of SARS-CoV-2 inhibitors.
Elucidating the molecular properties and anti-mycobacterial activity of cysteine peptidase domain of D29 mycobacteriophage endolysin
Authors: Gangakhedkar Rutuja , Jain Vikas
Published: September 2024

Emergence of antibiotic resistance in pathogenic
Mycobacterium tuberculosis
(
Mtb
) has elevated tuberculosis to a serious global threat, necessitating alternate solutions for its eradication. D29 mycobacteriophage can infect and kill several mycobacterial species including
Mtb
. It encodes an endolysin LysA to hydrolyze host bacteria peptidoglycan for progeny release. We previously showed that out of the two catalytically active domains of LysA [N-terminal domain (NTD) and lysozyme-like domain], NTD, when ectopically expressed in
Mycobacterium smegmatis
(
Msm
), is able to kill the bacterium nearly as efficiently as full-length LysA. Here, we dissected the functioning of NTD to develop it as a phage-derived small molecule anti-mycobacterial therapeutic. We performed a large-scale site-directed mutagenesis of the conserved residues in NTD and examined its structure, stability, and function using molecular dynamic simulations coupled with biophysical and biochemical experiments. Our data show that NTD functions as a putative cysteine peptidase with a catalytic triad composed of Cys41, His112, and Glu137, acting as nucleophile, base, and acid, respectively, and showing characteristics similar to the NlpC/P60 family of cysteine peptidases. Additionally, our peptidoglycan hydrolysis assays suggested that NTD hydrolyzes only mycobacterial peptidoglycan and does not act on Gram-positive and Gram-negative bacterial peptidoglycans. More importantly, the combined activity of exogenously added NTD and sub-lethal doses of anti-mycobacterial drugs kills
Msm in vitro
and exhibits disruption of pre-formed mycobacterial biofilm. We additionally show that NTD treatment increases the permeability of antibiotics in
Msm
, which reduces the minimum inhibitory concentration of the antibiotics. Collectively, we present NTD as a promising phage-derived therapeutic against mycobacteria.

IMPORTANCE

Mycobacteriophages are the viruses that use mycobacteria as host for their progeny production and, in the process, kill them. Mycobacteriophages are, therefore, considered as promising alternatives to antibiotics for killing pathogenic
Mycobacterium tuberculosis
. The endolysin LysA produced by mycobacteriophage D29 plays an important role in host cell lysis and virion release. Our work presented here highlights the functioning of LysA’s N-terminal catalytic domain (NTD) in order to develop it as phage-derived small molecule therapeutics. We show that combined treatment of exogenously added NTD and sub-lethal doses of anti-mycobacterial drugs kills
M. smegmatis
, shows synergism by reducing the minimum inhibitory concentration of these antibiotics, and exhibits disruption of pre-formed mature biofilm. These outcomes and our detailed biochemical and biophysical dissection of the protein further pave the way toward engineering and development of NTD as a promising therapeutic against mycobacterial infections such as tuberculosis.
Alterations in circulating immunoregulatory proteins discriminate poor CD4 T lymphocyte trajectories in people with HIV on suppressive antiretroviral therapy
Authors: Moar Preeti , Bowler Scott , Landay Alan L. , Gianella Sara , Ndhlovu Lishomwa C. , Premeaux Thomas A.
Published: September 2024

Despite the success in the management of HIV with antiretroviral therapy (ART), people with HIV (PWH) have a heightened state of immune activation and inflammation, and an estimated 10%–40% demonstrate poor CD4 T-cell reconstitution, thereby increasing their mortality and morbidity risk burden. Soluble immunoregulatory proteins that function in lymphocyte activation or inhibition are elevated in PWH and associate with T-cell dysfunction, HIV persistence, and are predictive of comorbid outcomes. Here, we measured a panel of 35 circulating immunoregulatory proteins in 116 PWH with variations in CD4 T-cell counts (poor CD4 trajectory: <200 cells/μl,
n
= 34 or immune competent: CD4 >500 cells/μl,
n
= 82) by Luminex. Participants were enrolled in the AIDS Clinical Trials Group Longitudinal Linked Randomized Trials cohort, had initiated ART on enrollment, and had been on suppressive ART for 1 year. Using non-parametric analysis, we found that the levels of CD276, ICOSL, BAFF, OX40, galectin-1, and galectin-9 were significantly higher in PWH with poor CD4 trajectories compared to individuals with immune-competent CD4 T-cell count. Notably, in logistic models, ICOSL and OX40 remained significant after adjusting for age and baseline plasma HIV RNA. Furthermore, Extreme Gradient Boosting machine learning models comprising co-stimulatory and inhibitory checkpoint proteins yielded high accuracy in classification of individuals with poor CD4 trajectories. In summary, we identified a novel signature of circulating immunoregulatory proteins indicative of poor CD4 trajectories that may serve as potential targets to monitor and manage immune perturbations more accurately in PWH during suppressive ART.

IMPORTANCE

It is essential to track immune perturbations related to insufficient CD4 T-cell recovery in PWH on suppressive ART as those with incomplete reconstitution are at a greater risk of non-AIDS-related morbidity and mortality. Several inflammatory soluble mediators have associated with poor immune reconstitution and adverse morbid outcomes in PWH, yet their implementation into routine clinical care to guide management remains inconsistent. Circulating immune checkpoint proteins have been linked to dysregulated immune pathways during suppressive ART and may serve as improved surrogate markers of clinical relevance. Here we investigate soluble lymphocyte-associated immunoregulatory proteins in virally suppressed PWH with no reported co-morbid outcomes and varying CD4 T-cell counts, to reveal underlying pathways that remain perturbed despite ART. This novel signature of immunoregulatory markers pertaining to poor CD4 T-cell trajectories uncover previously overlooked immune checkpoints as important targets for clinical monitoring of PWH in the setting of durable viral suppression by ART.
Genome-wide fitness analysis of
Salmonella enterica
reveals
aroA
mutants are attenuated due to iron restriction
in vitro
Authors: Rooke Jessica L. , Goodall Emily C. A. , Pullela Karthik , Da Costa Rochelle , Martinelli Nicole , Smith Chelsie , Mora Maria , Cunningham Adam F. , Henderson Ian R.
Published: September 2024

Salmonella enterica
is a globally disseminated pathogen that is the cause of over 100 million infections per year. The resulting diseases are dependent upon host susceptibility and the infecting serovar. As
S. enterica
serovar Typhimurium induces a typhoid-like disease in mice, this model has been used extensively to illuminate various aspects of
Salmonella
infection and host responses. Due to the severity of infection in this model, researchers often use strains of mice resistant to infection or attenuated
Salmonella
. Despite decades of research, many aspects of
Salmonella
infection and fundamental biology remain poorly understood. Here, we use a transposon insertion sequencing technique to interrogate the essential genomes of widely used isogenic wild-type and attenuated
S
. Typhimurium strains. We reveal differential essential pathways between strains
in vitro
and provide a direct link between iron starvation, DNA synthesis, and bacterial membrane integrity.

IMPORTANCE

Salmonella enterica
is an important clinical pathogen that causes a high number of deaths and is increasingly resistant to antibiotics. Importantly,
S. enterica
is used widely as a model to understand host responses to infection. Understanding how Salmonella survives
in vivo
is important for the design of new vaccines to combat this pathogen. Live attenuated vaccines have been used clinically for decades. A widely used mutation,
aroA
, is thought to attenuate
Salmonella
by restricting the ability of the bacterium to access particular amino acids. Here we show that this mutation limits the ability of
Salmonella
to acquire iron. These observations have implications for the interpretation of many previous studies and for the use of
aroA
in vaccine development.