bluuebunny/crossref_metadata_2025 huggingface dataset:
α‐costic acid, the main sesquiterpenoid isolated from Dittrichia viscosa (L) Greuter, induces oxidative stress and autophagy in tomato
Authors: Zanotti C. , Vurro M. , Evidente A. , Marra M.
Published: September 2024

Dittrichia viscosa (L.) Greuter, a perennial plant in the Asteraceae, has strong allelopathic activity due to the high content of various secondary metabolites. The bicyclic sesquiterpenoid α‐costic acid is the most abundant secondary metabolite of D. viscosa. Its remarkable insecticidal, antiparasitic, and phytotoxic activities point to its potential use as a natural herbicide, but information on its mode of action is lacking.

To shed light on the mechanism of action of α‐costic acid in plant cells, we investigated the phytotoxicity of α‐costic acid in tomato plants (Solanum lycopersicum L.) through in vivo assays, the underlying cellular effects using biochemical assays, and the effect on subcellular organelles using confocal microscopy on tomato protoplasts incubated with organelle‐specific fluorescent probes.

In vivo tests showed that α‐costic acid inhibited the growth of tomato seedlings and induced chlorosis and spot lesions in leaves. Biochemical assays demonstrated that α‐costic acid caused ion leakage, chlorophyll depletion, H2O2 overproduction, callose deposition, and membrane lipid peroxidation. Confocal microscopy demonstrated that α‐costic acid determined ROS overproduction and network disruption in mitochondria, singlet oxygen overproduction in chloroplasts, vacuole disintegration, and autophagosome formation.

Overall, our data are consistent with a model according to which α‐costic acid phytotoxicity is related to oxidative stress in mitochondria and chloroplasts that induces extensive membrane damage, ultimately resulting in cell death associated with autophagy
Image‐based crop disease detection using machine learning
Authors: Dolatabadian Aria , Neik Ting Xiang , Danilevicz Monica F. , Upadhyaya Shriprabha R. , Batley Jacqueline , Edwards David
Published: September 2024

Crop disease detection is important due to its significant impact on agricultural productivity and global food security. Traditional disease detection methods often rely on labour‐intensive field surveys and manual inspection, which are time‐consuming and prone to human error. In recent years, the advent of imaging technologies coupled with machine learning (ML) algorithms has offered a promising solution to this problem, enabling rapid and accurate identification of crop diseases. Previous studies have demonstrated the potential of image‐based techniques in detecting various crop diseases, showcasing their ability to capture subtle visual cues indicative of pathogen infection or physiological stress. However, the field is rapidly evolving, with advancements in sensor technology, data analytics and artificial intelligence (AI) algorithms continually expanding the capabilities of these systems. This review paper consolidates the existing literature on image‐based crop disease detection using ML, providing a comprehensive overview of cutting‐edge techniques and methodologies. Synthesizing findings from diverse studies offers insights into the effectiveness of different imaging platforms, contextual data integration and the applicability of ML algorithms across various crop types and environmental conditions. The importance of this review lies in its ability to bridge the gap between research and practice, offering valuable guidance to researchers and agricultural practitioners.
Phenotypic and phylogenetic analysis of Verticillium longisporum strains from European and Canadian oilseed rape fields
Authors: Vega‐Marin Marta , Obermeier Christian , Koopmann Birger , Zheng Xiaorong , Snowdon Rod , von Tiedemann Andreas
Published: September 2024

Verticillium longisporum is a vascular fungal pathogen of oilseed rape (OSR) that causes Verticillium stem striping. The pathogen segregates into three lineages originating from at least three hybridization events between four different Verticillium genomes, leading to the hybrid lineages A1/D1, A1/D2 and A1/D3. Although A1/D1 is considered the most relevant lineage in OSR, extensive studies addressing the geographical spread and phylogenetic relationships of Verticillium lineages are lacking. In the present study, the genetic diversity and relatedness of V. longisporum isolates from European and Canadian OSR fields were analysed. Based on genotyping by sequencing, genetic subgroups were identified and assigned to geographic origins and pathogenic traits. To assess the agronomic importance of different lineages, representative isolates were tested for pathogenicity and aggressiveness on OSR under greenhouse conditions. This study confirms that A1/D1 is the prevalent and most aggressive lineage of V. longisporum in European and Canadian OSR fields. Genetic clusters within the A1/D1 lineage were weakly correlated with geographic origin, but not with aggressiveness on winter OSR. Isolates from the United Kingdom, Latvia and Canada occurred only in a single and distinct subclade, indicating a more recent introduction, whereas isolates from locations where the disease has been known for a long time (France, Germany, Poland, Sweden) were less uniform and could be assigned to several subclades. Our results indicate that Verticillium stem striping in the United Kingdom, Latvia and Canada may have derived from separate and different single introductions of the pathogen in the recent past.
Proton Gradient Regulation 5 determines reserve partitioning between starch and lipids in C. reinhardtii
Authors: Saint‐Sorny Maureen , Dimitriades Alexandra , Delrue Florian , Johnson Xenie
Published: September 2024

Nutrient deprivation induces reserve accumulation in unicellular algae. An absence of nitrogen in the growth media results in the reorganization of the photosynthetic apparatus and triggers an increase in starch and triacylglyceride (TAG) accumulation in different algal species. Here we study the integration of photosynthetic regulatory mechanisms with carbon partitioning under N stress in C. reinhardtii. The mutant, proton gradient regulation 5 (pgr5) is impaired in photosynthetic cyclic electron flow resulting in low chloroplastic ATP/NADPH ratios. Over a time course, under both mixotrophic and phototrophic conditions, the pgr5 mutant did not accumulate starch in the first three days, but rather degraded its meagre reserves. In contrast, there was a high TAG content in the pgr5 mutant which we show, is not linked to a selective increase in autophagy in pgr5. In all strains, proteins involved in alternative electron pathways are upregulated while Photosystem II and chlorophyll are strongly degraded; pgr5 only preferentially preserved some cyt b6f complex. Our results show that low ATP/NADPH ratios due to an absence of cyclic electron flow in pgr5 result in the mobilization of starch and strong TAG accumulation from the onset of N stress in Chlamydomonas.
Sexual choking/strangulation and its association with condom and contraceptive use: Findings from a survey of students at a university in the Midwestern United States
Authors: Herbenick Debby , Fu Tsung‐Chieh , Patterson Perry Callie , Guerra‐Reyes Lucia , Eastman‐Mueller Heather , Svetina Valdivia Dubravka
Published: September 2024

Introduction

Consensual sexual choking has become prevalent among young United States (US) adults. In sex between women and men, women are overwhelmingly the ones choked, perhaps reproducing traditional heteronormative power dynamics. No research has examined the relationship between being choked during consensual sex and the use of external condoms and other contraceptives.

Methods

We administered a cross‐sectional campus‐representative survey to 4989 undergraduate students at a large public Midwestern US university.

Results

Half of respondents (n = 1803) had ever been choked during sex. Having been choked was associated with a significantly lower likelihood of event‐level condom use (OR = 0.32 [0.19, 0.54] for >5 times lifetime choking among men and OR = 0.35 [0.27, 0.45] for >5 times lifetime choking among women compared to those with no choking experiences) and in the past 6 months (OR = 0.42 [0.24, 0.72] for >5 times lifetime choking among men and OR = 0.59 [0.43, 0.81] for >5 times lifetime choking among women compared to those with no choking experiences). Also, having ever been choked was associated with a significantly greater likelihood of having used an implant/intra‐uterine device in the past 6 months (OR = 1.85 [1.28, 2.68] for >5 times lifetime choking compared to those with no choking experiences).

Conclusion

Recognition that sexual choking is prevalent among young people has only recently emerged and educational programs are lacking. Study findings could be used to engage people in discussions about choking in relation to gender, power, and reproductive health agency.
Thyroid Dysfunction and Alopecia Areata: A Genetic Prediction Causality Analysis Study
Authors: Zhao Yue , Guo Furong , Guo Mengyue
Published: September 2024

Background

Observational studies have suggested a correlation between alopecia areata (AA) and thyroid dysfunction (TD). However, the causal relationship between AA and TD remains uncertain. The purpose of this study is to investigate the causal relationship between these two conditions. Understanding the potential causal relationship between AA and TD is valuable for elucidating the pathogenesis of AA and for designing innovative methods to prevent and treat AA and its related complications.

Methods

All data for this two‐sample Mendelian randomization (MR) study were sourced from public databases. This study selected hypothyroidism, Hashimoto's thyroiditis, hyperthyroidism, subacute thyroiditis, and Graves' disease as exposure factors, with AA as the outcome variable. Data for hypothyroidism, Hashimoto's thyroiditis, hyperthyroidism, subacute thyroiditis, Graves' disease, and AA were obtained from related genome‐wide association studies (GWAS). Various MR analysis methods such as inverse variance weighted (IVW), MR‐Egger, and weighted median were utilized. Additionally, Cochrane's Q test was used to detect heterogeneity in MR results, and the MR‐Egger intercept test and MR pleiotropy residual sum and outlier (MR‐PRESSO) test were used to detect horizontal pleiotropy. A leave‐one‐out analysis was conducted to investigate the sensitivity of this association.

Results

We found statistically significant genetic predictions of AA with hypothyroidism, Hashimoto's thyroiditis, and subacute thyroiditis (IVW OR = 1.4009815, 95% confidence interval [CI]: 1.1210399–1.750829; p = 0.003030698, OR = 1.396101, 95% CI: 1.030134–1.89208; p = 0.03144273, OR = 0.732702, 95% CI: 0.604812–0.887634; p = 0.001483368). Furthermore, tests for pleiotropy showed no evidence of pleiotropy, enhancing the credibility of the study results. Finally, the leave‐one‐out test demonstrated the stability and robustness of this association.

Conclusion

This study provides new evidence of a potential genetic link between thyroid issues and AA. By employing the two‐sample MR method to eliminate confounding factors and reverse causation, unbiased results were obtained, confirming a causal relationship between hypothyroidism, Hashimoto's thyroiditis, subacute thyroiditis, and AA. This lays the foundation for further mechanistic studies and potential clinical applications. Future research should further explore the specific biological mechanisms between TD and the onset of AA.
Integrated genomic, transcriptomic, and metabolomic analyses of Ilex hylonoma provide insights into the triterpenoid saponin biosynthesis
Authors: Feng Landi , Yao Yingjun , Kang Minghui , Yang Wengjie , Han Yu , Liu Wei , Li Xiaonan , Li Na , Hu Yongqi , Liu Jianquan , Hu Quanjun
Published: September 2024

Ilex is known for its rich content of secondary metabolites, particularly triterpenoid saponins. These compounds hold significant value in natural remedies and herbal medicine. However, the molecular mechanisms responsible for triterpenoid biosynthesis in plants of this genus remain largely unexplored. In this study, we successfully generated the first chromosome‐scale genome of Ilex hylonoma. The assembly, comprising 20 anchored chromosomes, has an N50 contig size of 2.13 Mb and a scaffold size of 33.68 Mb. Comparative genome analyses with two other congeners with available chromosome‐level genomes suggested that an end‐to‐end chromosome fusion event likely contributed to the reduction in chromosome number from n = 20 to n = 19 within this genus. By integrating transcriptomic and metabolomic data, we identified the gene expression patterns and metabolite profiles of I. hylonoma across three commonly utilized medicinal tissues. We subsequently pinpointed candidate genes involved in the regulation of triterpenoid saponin biosynthesis, including CYP450 genes, UGT genes, and associated transcription factors. Furthermore, yeast heterologous expression analysis revealed that ihyl08363 catalyzed the conversion of β‐amyrin into oleanolic acid, while ihyl04303 catalyzed the C‐2α hydroxylation of oleanolic acid to produce maslinic acid. This integrated analysis provides valuable insights into the biosynthesis of important triterpenoid saponins in medicinal Ilex plants.
Establishment of mouse models for severe pulmonary hypertension through ‘double‐hit’ strategies
Authors: Chen Lingdan , Chen Xin , Huang Yuhang , Ma Zhuoji , Zeng Xiaohui , Wang Tao
Published: September 2024

Mouse models are crucial for understanding pulmonary hypertension (PH) mechanisms and developing therapies, but existing mouse models under hypoxia only exhibit mild PH. To address this, we established a double‐hit model combining unilateral pneumonectomy (LPx) or left pulmonary artery ligation (LPAL) with hypoxia exposure in C57BL/6 mice. Our detailed haemodynamic and histological evaluations post‐surgery demonstrated pronounced elevations in right ventricular systolic pressure (RVSP) (LPAL: 41.1 ± 4.63 mmHg, P = 0.005; LPx: 38.4 ± 2.95 mmHg, P = 0.002; Sham: 32.1 ± 2.21 mmHg) and pulmonary vascular wall thickness (LPAL: 56.9 ± 3.34%, P = 0.02; LPx: 54.3 ± 4.65%, P = 0.04; Sham: 44.8 ± 3.76%) compared to hypoxia‐exposed sham‐operated controls, reflecting a more severe PH phenotype. These novel models, which exhibit haemodynamic alterations akin to the established hypoxia with SU5416‐induced PH model as per published data, could offer a substantial contribution to future PH research and therapeutic development.
Experimental Application of a Method for Hidden Parameter Tracking in a Slowly Changing, Chaotic System
Authors: Cusumano J. P. , Chelidze D. , Chatterjee A.
Published: September 2024

Results are presented of an experimental application of a method for tracking hidden parameters in slowly changing chaotic systems. The method exploits the time scale separation between fast dynamic variables and a slow drifting parameter. Locally linear tracking models are constructed using data from the reference system sampled on a fast time scale, employing delay coordinate embedding. These reference models are used to track parameter drift. The method is successfully applied to a forced oscillator with a two-well potential. The effect of the choice of prediction time interval is studied. It is also observed that a simple correction for estimated modeling error gives a more sensitive tracking metric. For purposes of comparison with such model-based tracking methods, a heuristic method is also presented for detecting parameter changes using the autocorrelation function of the recorded time series. The relative merits of heuristic versus model-based techniques are discussed. Directions for future work are suggested.
Bubble Elimination Device in Hydraulic Systems
Authors: Suzuki Ryushi , Tanaka Yutaka , Yokota Shinichi
Published: September 2024

Bubbles in working fluids have much influence on the performance of hydraulic systems and cause some troubles. In this paper, the performance of the developed bubble elimination device concerning the effect of reducing the oil temperature rise is experimentally investigated. From a view point of energy balance in hydraulic systems, a simple mathematical model is proposed and validity of the model is studied.
On the Stability and Performance of Two-Stage Hydraulic Servovalves
Authors: Wright Heather , Alleyne Andrew , Liu Rui
Published: September 2024

In this work, a System Dynamics viewpoint is used to examine the stability and performance of a class of hydraulic devices. These devices use hydraulic amplification to command motion of large objects using relatively low level signals. A model is constructed and used for both analysis and simulation of system performance. The analysis is from a linear Classical Controls perspective and is found to be sufficient despite the nonlinear nature of the systems. The analysis is used to consider design changes to the valve components and their resulting effects. Even though the subsystems consist of stable individual components, their interconnection can lead to undesirable performance, or even instability, if the individual dynamics are improperly matched.
Numerical Simulation of Global Diffusive Mass Transfer in a Rotating-Wall Vessel Bioreactor
Authors: Gao Hongxia , Ayyaswamy Portonovo S. , Ducheyne Paul
Published: September 2024

The global diffusive mass transfer of different chemical species, specifically nutrition (glucose) and oxygen, in the fluid cell culture medium of the NASA designed Rotating-Wall Vessel (RWV) bioreactor has been numerically investigated. A finite difference method was employed to solve the governing equations for the species mass fraction fields. We have considered the 55 ml STLV and the 50 ml HARV as our domains of interest. The cell metabolic processes have been modeled as mass sinks absorbing oxygen and nutrition in the culture medium with time-dependent strengths. In one case studied, relative motion between the microcarrier and the fluid culture medium has been taken into account. The transient two-dimensional analysis employed here simulates the global mass diffusion process in the RWV. For the parameters considered here, the numerical results indicate that the HARV may be a better bioreactor for oxygen transport compared to the STLV.
Experimental and Analytical Studies of Heat Removal by Regionally Controlled Liquid-Cooled Garments
Authors: Shitzer Avraham
Published: September 2024

Space exploration, and particularly extravehicular activities, require creation of a “micro-climate” for the removal of metabolic heat. This is accomplished by a specially designed thermal garment. The early garments used by NASA for the Gemini program were air-ventilated. These proved to be inadequate and were subsequently replaced by water-air hybrid garments for the Apollo program (Chambers, 1970). These garments were made of flexible plastic tubes attached to a loosely-knit fabric. Cooled water circulated in the tubes which were in contact with the skin. Additionally, conditioned air flew across the outer layer of the fabric thereby removing sweat secreted.
Thermal Wave Propagation in a Thin Membrane Subjected to an Exponentially Growing/Decaying Wall Temperature
Authors: Tan Zhi-Ming , Yang Wen-Jei
Published: September 2024

Propagation of thermal waves in transient heat conduction in a very thin membrane is investigated by solving hyperbolic heat conduction equation. Analytical expressions are obtained for the temperature and heat flux distributions. Numerical computations are performed in order to determine the behavior of temperature and heat flux distributions in transient heat conduction. It is disclosed that in transient heat conduction, a heat pulse propagates as a wave and quickly begins to attenuate in the membrane, the peak of thermal waves has a sharp increase when the wavefronts from two sides meet at the centre of the membrane and collide with each other the first time and has an obvious decrease the second time. The results show that non-Fourier heat conduction is extremely significant with certain range of membrane thickness and duration time, and Fourier’s law used in macroscale heat conduction cannot be applied. The results also show that both temperature overshoot and temperature undershoot would occur in the membranes with smaller values of x0/(τC) within a very short period of time. The ranges of membrane thickness and duration time within which heat propagates as a wave are also determined.
Experimental Studies of the Heat Exchange in Paired Vessels Using the Rat Spinotrapezius Muscle
Authors: Song Ji , Xu Lisa X. , Lemons Daniel E. , Weinbaum Sheldon
Published: September 2024

Research on blood-tissue heat transfer in the past twenty years has focused on the question of where and how vascular heat transfer occurs. A number of different bioheat transfer models have been developed [1,3,5] to explain the mechanism of blood-tissue energy exchange. Among them Weinbaum et al. proposed that nearly all thermally significant vessels in skeletal muscle appeared as closely spaced countercurrent pairs, and the primary mechanism by which the microvascular blood flow altered the blood tissue heat transfer was incomplete countercurrent exchange in the thermally significant microvessels [5]. An effective thermal conductivity, keff, which is related to the local vascular geometry and blood flow, was therefore introduced to account for the enhancement of heat transfer due to the thermally significant vessels [4]. The characteristic thermal equilibration length, Lei, plays an important role in revealing the mechanism of microvascular heat transfer. It is a key feature of thermally significant vessels, but this length has not yet been experimentally determined. A better understanding of microvascular countercurrent heat exchange requires experimental confirmation of the thermal equilibration and keff.
Temperature Responses in the Canine Prostate During Transurethral Microwave Hyperthermia
Authors: Zhu Liang , Xu Lisa X. , Holmes Ken R.
Published: September 2024

In this research, experiments were performed to study the thermoregulation in the canine prostate during microwave hyperthermia. The transurethral thermal therapy (T3) system provided by Urologix, Inc. was used to impose microwave heating in the canine prostate. Five types of temperature responses to different microwave power levels as time varies, including both damped and sustained oscillatory temperature responses, have been observed. The decrease in prostatic tissue temperature during the microwave heating is believed to be caused by the increase of local blood flow, which was stimulated by the tissue temperature elevation. This work will help to provide a better understanding of the mechanism of how the temperature regulates within the canine prostate during transurethral microwave hyperthermia.
Cryopreservation of Cells Using Ultra-Rapid Freezing
Authors: Fowler Alex J. , Toner Mehmet
Published: September 2024

This paper reports on the development of a new cryopreservation protocol that uses laser warming and liquid nitrogen cooling to establish extreme temperature gradients that lead to cooling rates of greater than 106 K per second. Experiments using short laser pulses demonstrate that these cooling rates lead to the creation of clear ice regions consistent with the creation of amorphous ice. Differential thermal analysis of the clear ice regions proves that they do consist of substantial portions of amorphous ice. It is believed that freezing cells in a non-crystalline ice will lead to successful cryopreservation of any cell type. Numerical simulations have allowed investigators to identify a geometry that will enable the freezing of cells and small tissue samples into an amorphous solid phase with the use of little or no cryoprotectant.
Perturbations of Large Vessels on Induced Temperature Distributions: Part A — Three-Dimensional Simulation Study
Authors: Craciunescu Oana , Clegg Scott T.
Published: September 2024

It is well known that large blood vessels perturb the induced temperature distributions in biological situations. The understanding of the magnitude of the perturbation of the temperature distribution as a function of the vessel size and temperature gradient are critical to the development of accurate (and useful) models of bioheat transport. Weinbaum et al. have demonstrated a method for measuring the temperature distribution due to the presence of “small vessels”. However, this technique is highly invasive and therefore not generally useful. An alternative to this method, is the use of a combination of MR image techniques to noninvasively measure 1) the location, size and velocity of certain blood vessels, and 2) the induced temperature distribution. This paper describes the principle of this method. Numerical simulations are to be used to evaluate the accuracy of the MR technique with particular emphasis on the perturbation around blood vessels. Prior to the evaluation of the accuracy of the MR technique, the accuracy of the numerical method must be determined. This paper reports on the numerical simulations performed for an inhomogeneous perfused phantom that resembles the phantom used in the experimental setup. The results agree with previously published data.
Stress Analysis of Bolted Joints Using Hexagon Bolts With Flanges and Estimation of Axial Bolt Load
Authors: Yasui Hajime , Sawa Toshiyuki , Motegi Youich
Published: September 2024

The contact stress distributions at the bearing surfaces between the bolt head with flange washer and clamped parts (hollow cylinder) are analyzed using axisymmetric theory of elasticity as a four-body contact problem. In the analysis, bolt head, flange washer and the bolt shaft are replaced with finite solid cylinders. In the numerical calculations, the effect of the dimensions of the flanges in hexagon bolts and the clamped parts (hollow cylinder) on the contact stress distributions are clarified. The contact stress distributions of bolted joints using hexagon bolts with flange washers are compared with those using hexagon bolts without flange washers. In addition, the equivalent length of the deformation in the bolt head with the flange is proposed in order to calculate the spring constant of bolt-nut system. Furthermore, a method for estimating an axial bolt force is proposed using the deformation of the bolt head. The deformations of bolt head in bolted joints using hexagon bolts with flange washers were measured with a surface roughness meter and the axial bolt load was measured with strain gauges. The estimated results are in fairly good agreement with the measured results.
Exogenous Glucose Oxidation During Exercise Is Positively Related to Body Size
Authors: Ijaz Abdullah , Collins Adam J. , Moreno-Cabañas Alfonso , Bradshaw Louise , Hutchins Katie , Betts James A. , Podlogar Tim , Wallis Gareth A. , Gonzalez Javier T.
Published: September 2024

There is little evidence that body size alters exogenous glucose oxidation rates during exercise. This study assessed whether larger people oxidize more exogenous glucose during exercise than smaller people. Fifteen cyclists were allocated into two groups based on body mass (SMALL, <70 kg body mass, n = 9, two females) or (LARGE, >70 kg body mass, n = 6) matched for lactate threshold (SMALL: 2.3 ± 0.4 W/kg, LARGE: 2.3 ± 0.3 W/kg). SMALL completed 120 min of cycling at 95% of lactate threshold1. LARGE completed two trials in a random order, one at 95% of lactate threshold1 (thereby exercising at the same relative intensity [RELATIVE]) and one at an absolute intensity matched to SMALL (ABSOLUTE). In all trials, cyclists ingested 90 g/hr of 13C-enriched glucose. Total exogenous glucose oxidation was (mean ± SD) 33 ± 8 g/hr in SMALL versus 45 ± 13 g/hr in LARGE-RELATIVE (mean difference: 13 g/hr, 95% confidence interval [2, 24] g/hr, p = .03). Large positive correlations were observed for measures of exogenous carbohydrate oxidation versus body size (body mass, height, and body surface area; e.g., body surface area vs. peak exogenous glucose oxidation, r = .85, 95% confidence interval [.51, .95], p < .01). When larger athletes reduced the intensity from RELATIVE to ABSOLUTE, total exogenous glucose oxidation was 39 ± 7 g/hr (p = .43 vs. LARGE-RELATIVE). In conclusion, the capacity for exogenous glucose oxidation is, on average, higher in larger athletes than smaller athletes during exercise. The extent to which this is due to higher absolute exercise intensity requires further research, but body size may be a consideration in tailoring sports nutrition guidelines for carbohydrate intake during exercise.
Standing Still or Standing Out: Distinguishing Passive and Active Standing Is a Step in the Right Direction
Authors: Shivgulam Madeline E. , MacDonald Emily E. , Waghorn Jocelyn , O’Brien Myles W.
Published: September 2024

Standing is a solution to reduce or break-up sedentary time (sitting/reclining/lying while awake); however, the measurable health benefits of standing are conflicting. A recent article in the Journal for the Measurement of Physical Behaviour has demonstrated that the thigh-worn activPAL inclinometer can distinguish between passive (no movement) and active (structured micromovements) standing using a machine learning model in lab-based and free-living environments. The predictive model extends beyond previous research by considering three-dimensional aspects of movement into the decision tree model. The ability to characterize these distinct postures is increasingly important to understand the physiological difference between passive and active standing. Notably, active standing, when stepping is not feasible, may be superior to passive standing for improving metabolic activity, reducing fatigue, and enhancing blood flow. Applied to free-living settings, active standing could help mitigate or attenuate some adverse cardiometabolic effects of stationary activity, thereby yielding positive cardiovascular outcomes. As standing gains recognition as a potentially important health behavior, distinguishing between passive and active standing offers a unique opportunity to clarify the health impacts of standing time, contributing to the evidence base. This evidence may contribute to more detailed activity guidelines and support public health initiatives to promote active standing. These advancements have the potential to enhance our understanding of standing behaviors’ health impacts and the possible divergent physiological effects of active versus passive standing.
Greenland Norse walrus exploitation deep into the Arctic
Authors: Ruiz-Puerta Emily J. , Jarrett Greer , McCarthy Morgan L. , Pan Shyong En , Keighley Xénia , Aiken Magie , Zampirolo Giulia , Loonen Maarten J. J. E. , Gotfredsen Anne Birgitte , Howse Lesley R. , Szpak Paul , Pálsson Snæbjörn , Rufolo Scott , Malmquist Hilmar J. , Desjardins Sean P. A. , Olsen Morten Tange , Jordan Peter D.
Published: September 2024

Walrus ivory was a prized commodity in medieval Europe and was supplied by Norse intermediaries who expanded across the North Atlantic, establishing settlements in Iceland and Greenland. However, the precise sources of the traded ivory have long remained unclear, raising important questions about the sustainability of commercial walrus harvesting, the extent to which Greenland Norse were able to continue mounting their own long-range hunting expeditions, and the degree to which they relied on trading ivory with the various Arctic Indigenous peoples that they were starting to encounter. We use high-resolution genomic sourcing methods to track walrus artifacts back to specific hunting grounds, demonstrating that Greenland Norse obtained ivory from High Arctic waters, especially the North Water Polynya, and possibly from the interior Canadian Arctic. These results substantially expand the assumed range of Greenland Norse ivory harvesting activities and support intriguing archaeological evidence for substantive interactions with Thule Inuit, plus possible encounters with Tuniit (Late Dorset Pre-Inuit).
Soil nitrogen-related functional genes undergo abundance changes during vegetation degradation in a Qinghai-Tibet Plateau wet meadow
Authors: Du Jianan , Ma Weiwei , Li Guang , Chang Wenhua , Chun Longyong
Published: September 2024

Climate change and anthropogenic activities have significantly contributed to the degradation of wet meadows on the Qinghai-Tibet Plateau (QTP). Soil nitrogen (N) availability is a crucial determinant of the productivity of wet meadow vegetation. Furthermore, soil microbial nitrogen functional genes (NFGs) are critical in the transformation of soil N. Nevertheless, the dynamics of NFGs in response to vegetation degradation, as well as the underlying drivers, remain poorly understood. In this study, wet meadows at varying levels of vegetation degradation on the QTP, categorized as non-degraded (ND), slightly degraded (SD), moderately degraded (MD), and heavily degraded (HD), were examined. Soil samples from depths of 0 to 10 cm and 10 to 20 cm were collected during different growth cycles (June 2020, August 2020, and May 2021). The analysis focused on NFGs involved in organic nitrogen fixation (
nifH
), archaeal and bacterial ammonia oxidation (
amoA-AOA
and
amoA-AOB
, respectively), and nitrite reduction (
nirK
), utilizing real-time fluorescence quantitative PCR. Our findings indicate a significant decline in the abundance of NFGs with intensified vegetation degradation, exhibiting notable spatial and temporal fluctuations. Specifically, the relative NFGs followed the pattern:
nirK
>
amoA-
AOA >
amoA-
AOB >
nifH
. Redundancy analysis revealed that vegetation cover was the primary regulator of NFGs abundance, accounting for 56.1%–57% of the variation. Additionally, soil total nitrogen, pH, and total phosphorus content were responsible for 38.5%, 28.2%, and 7% of the variability in NFGs, respectively. The (
amoA-AOA + amoA-AOB + nirK
) ratios associated with effective N transformation indicated that the vegetation degradation process moderately increased the nitrification potential.

IMPORTANCE

Our research investigates how the degradation of meadows affects the tiny organisms in soil that help plants use nitrogen, which is essential for their growth. In the Qinghai-Tibet Plateau, a region known for its unique ecosystems, we found that as meadows deteriorate—due to climate change and human activities—the number of these beneficial organisms significantly decreases. This decline could reduce soil fertility, impacting plant life and the overall health of the ecosystem. Understanding these changes helps us grasp how environmental pressures influence soil and plant health. Such knowledge is crucial for developing strategies to preserve these vulnerable ecosystems and ensure they continue to sustain biodiversity and provide resources for local communities.
The hindgut microbiota of coconut rhinoceros beetles (
Oryctes rhinoceros
) in relation to their geographical populations
Authors: Han Chiao-Jung , Huang Jen-Pan , Chiang Min-Rou , Jean Ok Shin Malagayo , Nand Nitesh , Etebari Kayvan , Shelomi Matan
Published: September 2024

The coconut rhinoceros beetle (CRB,
Oryctes rhinoceros
) is a palm tree pest capable of rapidly expanding its population in new territories. Previous studies identified a digestive symbiosis between CRB and its gut microbes. However, no research compared the genetic variation of CRBs with their hindgut microbiota on a global scale. This study aims to investigate the genetic divergence of CRB and the compositional variation of CRB’s microbiota across different geographical locations, and explore the association between them and their predicted functional profiles and environmental data. The research reveals a distinct and consistent microbial community within local populations, but it varies across different geographical populations. The microbial functional profiles linked to the production of digestive enzymes, including cellulases and ligninases, are nonetheless globally conserved. This suggests that CRBs employ specific mechanisms to select and maintain microbes with functional benefits, contributing to host adaptability, stress tolerance, and fitness. The CRB microbial communities did not appear to recapitulate the genetic variation of their hosts. Rather than depend on obligate symbionts, CRBs seem to establish similar digestive associations with whatever environmentally acquired microbes are available wherever they are, aiding them in successfully establishing after invading a new location.

IMPORTANCE

Coconut rhinoceros beetles (CRBs) are notorious pests on Arecaceae plants, posing destructive threats to countries highly reliant on coconut, oil palm, and date palm as economic crops. In the last century, CRBs have rapidly expanded their presence to territories that were once free of these beetles. The United States, for instance, has officially designated CRBs as invasive and alien pests. Given their remarkable ability to swiftly adapt to new environments, their gut microbes may play a crucial role in this process. While the microbiota of CRBs vary depending on geographical location, these beetles consistently exhibit a functionally identical digestive association with locally acquired microbes. This underscores the significance of CRB-microbe association in shaping the adaptive strategies of this agricultural pest.
Discovery of a novel methionine biosynthetic route
via O
-phospho-
l
-homoserine
Authors: Hasebe Fumihito , Adachi Kazuya , Maruyama Chitose , Hamano Yoshimitsu
Published: September 2024

Methionine (Met), a sulfur-containing amino acid, is essential for the underlying biological processes in living organisms. In addition to its importance as a starting building block for peptide chain elongation in protein biosynthesis, Met is a direct precursor of
S
-adenosyl-
l
-methionine, an indispensable methyl donor molecule in primary and secondary metabolism.
Streptomyces
bacteria are well known to produce diverse secondary metabolites, but many strains lack canonical Met pathway genes for
l
-homocysteine, a direct precursor of Met in bacteria, plants, and archaea. Here, we report the identification of a novel gene (
metM
) responsible for the Met biosynthesis in
Streptomyces
strains and demonstrate the catalytic function of the gene product, MetM. We further identified the
metO
gene, a downstream gene of
metM
, and showed that it encodes a sulfur-carrier protein (SCP). In
in vitro
analysis, MetO was found to play an important role in a sulfur donor by forming a thiocarboxylated SCP. Together with MetO (thiocarboxylate), MetM directly converted
O
-phospho-
l
-homoserine to
l
-homocysteine.
O
-Phospho-
l
-homoserine is also known as an intermediate for threonine biosynthesis in bacteria and plants, and MetM shares sequence homology with threonine synthase. Our findings thus revealed that MetM seizes
O
-phospho-
l
-homoserine from the threonine biosynthetic pathway and uses it as an intermediate of the Met biosynthesis to generate the sulfur-containing amino acid. Importantly, this MetM/MetO pathway is highly conserved in
Streptomyces
bacteria and distributed in other bacteria and archaea.

IMPORTANCE

Methionine (Met) is a sulfur-containing proteinogenic amino acid. Moreover, Met is a direct precursor of
S
-adenosyl-
l
-methionine, an indispensable molecule for expanding the structural diversity of natural products. Because Met and its derivatives benefit humans, the knowledge of Met biosynthesis is important as a basis for improving their fermentation.
Streptomyces
bacteria are well known to produce diverse and valuable natural products, but many strains lack canonical Met pathway genes. Here, we identified a novel
l
-homocysteine synthase (MetM) in
Streptomyces
and demonstrated that it converts
O
-phospho-L-homoserine to
l
-homocysteine using a thiocarboxylated sulfur-carrier protein as a sulfur donor. Since the
metM
is distributed in other bacteria and archaea, our pioneering study contributes to understanding Met biosynthesis in these organisms.
Bacterial amino acid chemotaxis: a widespread strategy with multiple physiological and ecological roles
Authors: Matilla Miguel A. , Krell Tino
Published: September 2024

Chemotaxis is the directed, flagellum-based movement of bacteria in chemoeffector gradients. Bacteria respond chemotactically to a wide range of chemoeffectors, including amino, organic, and fatty acids, sugars, polyamines, quaternary amines, purines, pyrimidines, aromatic hydrocarbons, oxygen, inorganic ions, or polysaccharides. Most frequent are chemotactic responses to amino acids (AAs), which were observed in numerous bacteria regardless of their phylogeny and lifestyle. Mostly chemoattraction responses are observed, although a number of bacteria are repelled from certain AAs. Chemoattraction is associated with the important metabolic value of AAs as growth substrates or building blocks of proteins. However, additional studies revealed that AAs are also sensed as environmental cues. Many chemoreceptors are specific for AAs, and signaling is typically initiated by direct ligand binding to their four-helix bundle or dCache ligand-binding domains. Frequently, bacteria possess multiple AA-responsive chemoreceptors that at times possess complementary AA ligand spectra. The identification of sequence motifs in the binding sites at dCache_1 domains has permitted to define an AA-specific family of dCache_1AA chemoreceptors. In addition, AAs are among the ligands recognized by broad ligand range chemoreceptors, and evidence was obtained for chemoreceptor activation by the binding of AA-loaded solute-binding proteins. The biological significance of AA chemotaxis is very ample including in biofilm formation, root and seed colonization by beneficial bacteria, plant entry of phytopathogens, colonization of the intestine, or different virulence-related features in human/animal pathogens. This review provides insights that may be helpful for the study of AA chemotaxis in other uncharacterized bacteria.
HCV infection activates the proteasome via PA28γ acetylation and heptamerization to facilitate the degradation of RNF2, a catalytic component of polycomb repressive complex 1
Authors: Kasai Hirotake , Yamashita Atsuya , Akaike Yasunori , Tanaka Tomohisa , Matsuura Yoshiharu , Moriishi Kohji
Published: September 2024

We previously reported that hepatitis C virus (HCV) infection or HCV core protein expression induces HOX gene expression by impairing histone H2A monoubiquitination via a proteasome-dependent reduction in the level of RNF2, a key catalytic component of polycomb repressive complex 1 (H. Kasai, K. Mochizuki, T. Tanaka, A. Yamashita, et al., J Virol 95:e01784-20, 2021,
https://doi.org/10.1128/jvi.01784-20
). In this study, we aimed to investigate the mechanism by which HCV infection accelerates RNF2 degradation. Yeast two-hybrid screening and an immunoprecipitation assay revealed that RNF2 is a PA28γ-binding protein. The proteasome activator PA28γ destabilized the RNF2 protein in a proteasome-dependent manner, since RNF2 degradation was impaired by PA28γ knockout or MG132 treatment. HCV infection or core protein expression reduced the levels of RNF2 and histone H2A K119 monoubiquitination and induced the expression of HOX genes in the presence of PA28γ, while PA28γ knockout reversed these changes. Treatment with a lysine acetyltransferase inhibitor inhibited the acetylation of PA28γ at K195 and the degradation of the RNF2 protein, while treatment with a lysine deacetylase inhibitor accelerated these events in a PA28γ-dependent manner. RNF2 protein degradation was increased by expression of the acetylation mimetic PA28γ mutant but not by expression of the acetylation-defective mutant or the proteasome activation-defective mutant. Furthermore, HCV infection or core protein expression facilitated the interaction between PA28γ and the lysine acetyltransferase CBP/p300 and then accelerated PA28γ acetylation and heptazmerization to promote RNF2 degradation. These data suggest that HCV infection accelerates the acetylation-dependent heptamerization of PA28γ to increase the proteasomal targeting of RNF2.

IMPORTANCE

HCV is a causative agent of HCV-related liver diseases, including hepatic steatosis, cirrhosis, and hepatocellular carcinoma. PA28γ, which, in heptameric form, activates the 20S core proteasome for the degradation of PA28γ-binding proteins, is responsible for HCV-related liver diseases. HCV core protein expression or HCV infection accelerates RNF2 degradation, leading to the induction of HOX gene expression via a decrease in the level of H2Aub on HOX gene promoters. However, the mechanism of RNF2 degradation in HCV-infected cells has not been clarified. The data presented in this study suggest that PA28γ acetylation and heptamerization are promoted by HCV infection or by core protein expression to activate the proteasome for the degradation of RNF2 and are responsible for HCV propagation. This study provides novel insights valuable for the development of therapies targeting both HCV propagation and HCV-related diseases.
The feasibility of establishing a hamster model for HBV infection:
in vitro
evidence
Authors: Zhang Hu , Liu Yanan , Liu Cheng-Der , Wang Zhongde , Guo Haitao
Published: September 2024

Chronic hepatitis B virus (HBV) infection remains a significant public health burden with no cure currently available. The research to cure HBV has long been hampered by the lack of immunocompetent small animal models capable of supporting HBV infection. Here, we set out to explore the feasibility of the golden Syrian hamster as an immunocompetent small rodent model for HBV infection. We first started with
in vitro
assessments of the HBV replication cycle in primary hamster hepatocytes (PHaHs) by adenoviral HBV (Ad-HBV) transduction. Our results demonstrated that PHaHs support HBV reverse transcription and subsequent cccDNA formation via the intracellular recycling pathway. Next, with luciferase reporter assays, we confirmed that PHaHs support the activities of all HBV major promoters. Then, we transduced PHaHs with an adenoviral vector expressing HBV receptor human Na+/taurocholate cotransporting polypeptide NTCP (Ad-huNTCP), followed by HBV inoculation. While the untransduced PHaHs did not support HBV infection, Ad-huNTCP-transduced PHaHs supported
de novo
cccDNA formation, viral mRNA transcription, and expression of viral antigens. We then humanized the amino acid (aa) residues of hamster NTCP (haNTCP) critical for HBV entry, aa84-87 and aa157-165, and transfected HepG2 cells with constructs expressing wild-type haNTCP and humanized-haNTCP, H84R/P87N and H84R/P87N/G157K/M160V/M165L, respectively, followed by HBV inoculation. The results showed that the humanization of H84R/P87N alone was sufficient to support HBV infection at a level comparable to that supported by huNTCP. Taken together, the above
in vitro
evidence supports the future direction of humanizing haNTCP for HBV infection
in vivo
.

IMPORTANCE

One of the biggest challenges in developing an HBV cure is the lack of immunocompetent animal models susceptible to HBV infection. Developing such models in mice has been unsuccessful due to the absence of a functional HBV receptor, human NTCP (huNTCP), and the defect in supporting viral cccDNA formation. In search of alternative models, we report herein multiple lines of
in vitro
evidence for developing a golden Syrian hamster model for HBV infection. We demonstrate that the primary hamster hepatocytes (PHaHs) support HBV replication, transcription, and cccDNA formation, and PHaHs are susceptible to
de novo
HBV infection in the presence of huNTCP. Furthermore, expressing hamster NTCP with two humanized residues critical for HBV entry renders HepG2 cells permissive to HBV infection. Thus, our work lays a solid foundation for establishing a gene-edited hamster model that expresses humanized NTCP for HBV infection
in vivo
.
Genome sequence of
Pseudomonas silesiensis
strain G3, a member of a bacterial consortium capable of polyethylene degradation
Authors: Schneider Beate , Pfeiffer Friedhelm , Remus Daniela , Dyall-Smith Mike , Kunte Hans-Jörg
Published: September 2024

A consortium of landfill bacteria including strain G3 can break down polyethylene, a long-lasting plastic that accumulates in the environment. The complete genome sequence of strain G3 was determined by PacBio and Nanopore sequencing and consists of three circular replicons. Genome-based classification assigned strain G3 to the species
Pseudomonas silesiensis
.