bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification and Profiling of Histone Acetyltransferase Substrates by Bioorthogonal Labeling
Authors: Song Jiabao , Han Zhen , Zheng Y. George 
Published: July 2022

AbstractHistone acetyltransferases (HATs, also known as lysine acetyltransferases, KATs) catalyze acetylation of their cognate protein substrates using acetyl‐CoA (Ac‐CoA) as a cofactor and are involved in various physiological and pathological processes. Advances in mass spectrometry‐based proteomics have allowed the discovery of thousands of acetylated proteins and the specific acetylated lysine sites. However, due to the rapid dynamics and functional redundancy of HAT activities, and the limitation of using antibodies to capture acetylated lysines, it is challenging to systematically and precisely define both the substrates and sites directly acetylated by a given HAT. Here, we describe a chemoproteomic approach to identify and profile protein substrates of individual HAT enzymes on the proteomic scale. The approach involves protein engineering to enlarge the Ac‐CoA binding pocket of the HAT of interest, such that a mutant form is generated that can use functionalized acyl‐CoAs as a cofactor surrogate to bioorthogonally label its protein substrates. The acylated protein substrates can then be chemoselectively conjugated either with a fluorescent probe (for imaging detection) or with a biotin handle (for streptavidin pulldown and chemoproteomic identification). This modular chemical biology approach has been successfully implemented to identify protein substrates of p300, GCN5, and HAT1, and it is expected that this method can be applied to profile and identify the sub‐acetylomes of many other HAT enzymes. © 2022 Wiley Periodicals LLC.Basic Protocol 1: Labeling HAT protein substrates with azide/alkyne‐biotinAlternate Protocol: Labeling protein substrates of HATs with azide/alkyne‐TAMRA for in‐gel visualizationSupport Protocol 1: Expression and purification of HAT mutantsSupport Protocol 2: Synthesis of Ac‐CoA surrogatesBasic Protocol 2: Streptavidin enrichment of biotinylated HAT substratesBasic Protocol 3: Chemoproteomic identification of HAT substratesBasic Protocol 4: Validation of specific HAT substrates with western blotting
Biomass‐Based N‐Rich Porous Carbon Materials for CO2 Capture and in‐situ Conversion
Authors: Xie Wei‐Hang , Yao Xiangyang , Li Heng , Li Hong‐Ru , He Liang‐Nian 
Published: July 2022

AbstractCapturing CO2 and subsequently converting into valuable chemicals has attracted extensive attention. Herein, a series of biomass‐based N‐rich porous carbon materials with high specific surface area and pore volume were prepared using biomass waste soybean dregs as precursors. The nitrogen content was up to 4 % with different forms in the carbon skeleton such as pyridine‐N, pyrrole‐N. The synergistic effect of ultra‐micropore (pore size <0.7 nm) and N‐containing groups endowed the materials with a high CO2 adsorption capacity, reaching 6.3 and 3.6 mmol g−1 at 0 and 25 °C under atmospheric pressure, respectively. In addition, the sufficient interaction between N‐containing groups and CO2 was demonstrated by solid‐state nuclear magnetic resonance spectroscopy, and the captured CO2 was possibly activated in the form of carbamate, which is conducive to subsequent conversion. Therefore, the supported catalyst with the as‐synthetic porous carbon material as the carrier and ZnII as catalytic sites was prepared and successfully applied for carboxylative cyclization of propargylic amine with CO2 to afford the 3‐benzyl‐5‐methyleneoxazolidin‐2‐one. The results showed that CO2 capture and in‐situ conversion work effectively to produce highly value‐added chemicals. In this process, the captured CO2 could be activated and fixed into chemicals in mild conditions. More importantly, the energy consumption in CO2 desorption and adsorbent regeneration could be avoided. The valorization of both solid waste and CO2 to valuable chemicals provides an elegant strategy of killing three birds with one stone.
Reproduction in deep‐sea vent shrimps is influenced by diet, with rhythms apparently unlinked to surface production
Authors: Methou Pierre , Chen Chong , Kayama Watanabe Hiromi , Cambon Marie‐Anne , Pradillon Florence 
Published: July 2022

AbstractVariations in offspring production according to feeding strategies or food supply have been recognized in many animals from various ecosystems. Despite an unusual trophic structure based on non‐photosynthetic primary production, these relationships remain largely under‐studied in chemosynthetic ecosystems. Here, we use Rimicaris shrimps as a study case to explore relationships between reproduction, diets, and food supply in these environments. For that, we compared reproductive outputs of three congeneric shrimps differing by their diets. They inhabit vents located under oligotrophic waters of tropical gyres with opposed latitudes, allowing us to also examine the prevalence of phylogenetic vs environmental drivers in their reproductive rhythms. For this, we used both our original data and a compilation of published observations on the presence of ovigerous females covering various seasons over the past 35 years. We report distinct egg production trends between Rimicaris species relying solely on chemosymbiosis—R. exoculata and R. kairei—and one relying on mixotrophy, R. chacei. Besides, our data suggest a reproductive periodicity that does not correspond to seasonal variations in surface production, with substantial proportions of brooding females during the same months of the year, despite those months corresponding to either boreal winter or austral summer depending on the hemisphere. These observations contrast with the long‐standing paradigm in deep‐sea species for which periodic reproductive patterns have always been attributed to seasonal variations of photosynthetic production sinking from the surface. Our results suggest the presence of an intrinsic basis for biological rhythms in the deep sea, and bring to light the importance of having year‐round observations in order to understand the life history of vent animals.
Genetic diversity of Diaphorina citri (Hemiptera: Liviidae) unravels phylogeographic structure and invasion history of eastern African populations
Authors: Ajene Inusa Jacob , Khamis Fathiya Mbarak , van Asch Barbara , Pietersen Gerhard , Seid Nurhussen , Wairimu Anne Wambui , Ombura Fidelis Levi , Akutse Komivi Senyo , Sétamou Mamoudou , Subramanian Sevgan , Mohammed Samira , Ekesi Sunday 
Published: July 2022

AbstractThe Asian citrus psyllid (Diaphorina citri Kuwayama) is a key pest of Citrus sp. worldwide, as it acts as a vector for Candidatus Liberibacter asiaticus, the bacterial pathogen that causes citrus Huanglongbing. Diaphorina citri has been reported in Kenya, Tanzania, and more recently in Ethiopia. This study assessed the genetic diversity and phylogeographic structure of the pest to gain insights into the potential sources of its introduction into Africa. Population structure and differentiation of D. citri populations from China, Ethiopia, Kenya, Tanzania, and the USA were assessed using 10 microsatellite loci. Additionally, five new complete mitogenomes of D. citri collected in China, Ethiopia, Kenya, Tanzania, and the USA were analyzed in the context of publicly available sequences. Genotype data grouped the D. citri populations from Kenya and Tanzania in one cluster, and those from Ethiopia formed a separate cluster. The two genetic clusters inferred from genotype data were congruent with mitochondrial sequence data. The mitogenomes from Kenya/Tanzania/China had 99.0% similarity, and the Ethiopia/USA had 99.9% similarity. In conclusion, D. citri populations in eastern Africa have different sources, as the Kenyan and Tanzanian populations probably originated from southeastern Asia, while the Ethiopian population most probably originated from the Americas.
Behavioral “bycatch” from camera trap surveys yields insights on prey responses to human‐mediated predation risk
Authors: Burton A. Cole , Beirne Christopher , Sun Catherine , Granados Alys , Procko Michael , Chen Cheng , Fennell Mitchell , Constantinou Alexia , Colton Chris , Tjaden‐McClement Katie , Fisher Jason T. , Burgar Joanna 
Published: July 2022

AbstractHuman disturbance directly affects animal populations and communities, but indirect effects of disturbance on species behaviors are less well understood. For instance, disturbance may alter predator activity and cause knock‐on effects to predator‐sensitive foraging in prey. Camera traps provide an emerging opportunity to investigate such disturbance‐mediated impacts to animal behaviors across multiple scales. We used camera trap data to test predictions about predator‐sensitive behavior in three ungulate species (caribou Rangifer tarandus; white‐tailed deer, Odocoileus virginianus; moose, Alces alces) across two western boreal forest landscapes varying in disturbance. We quantified behavior as the number of camera trap photos per detection event and tested its relationship to inferred human‐mediated predation risk between a landscape with greater industrial disturbance and predator activity and a “control” landscape with lower human and predator activity. We also assessed the finer‐scale influence on behavior of variation in predation risk (relative to habitat variation) across camera sites within the more disturbed landscape. We predicted that animals in areas with greater predation risk (e.g., more wolf activity, less cover) would travel faster past cameras and generate fewer photos per detection event, while animals in areas with less predation risk would linger (rest, forage, investigate), generating more photos per event. Our predictions were supported at the landscape‐level, as caribou and moose had more photos per event in the control landscape where disturbance‐mediated predation risk was lower. At a finer‐scale within the disturbed landscape, no prey species showed a significant behavioral response to wolf activity, but the number of photos per event decreased for white‐tailed deer with increasing line of sight (m) along seismic lines (i.e., decreasing visual cover), consistent with a predator‐sensitive response. The presence of juveniles was associated with shorter behavioral events for caribou and moose, suggesting greater predator sensitivity for females with calves. Only moose demonstrated a positive behavioral association (i.e., longer events) with vegetation productivity (16‐day NDVI), suggesting that for other species bottom‐up influences of forage availability were generally weaker than top‐down influences from predation risk. Behavioral insights can be gleaned from camera trap surveys and provide complementary information about animal responses to predation risk, and thus about the indirect impacts of human disturbances on predator–prey interactions.
Dietary characterization of the endangered salt marsh harvest mouse and sympatric rodents using DNA metabarcoding
Authors: Aylward Cody M. , Statham Mark J. , Barthman‐Thompson Laureen , Kelt Douglas A. , Sacks Benjamin N. 
Published: July 2022

AbstractThe salt marsh harvest mouse (Reithrodontomys raviventris; RERA) is an endangered species endemic to the coastal wetlands of the San Francisco Estuary, California. RERA are specialized to saline coastal wetlands, and their historical range has been severely impacted by landscape conversion and the introduction of non‐native plant and rodent species. A better understanding of their diet is needed to assess habitat quality, particularly in relation to potential competitors. We investigated three questions using DNA metabarcoding with ITS2 and trnL markers: (1) Do RERA specialize on the native plant, pickleweed (Salicornia pacifica), (2) Do RERA consume non‐native plants, and (3) What is the dietary niche breadth and overlap with three sympatric native and non‐native rodents? RERA diet was dominated by two plants, native Salicornia and non‐native salt bush (Atriplex spp.), but included 48 plant genera. RERA diet breadth was narrowest in fall, when they consumed the highest frequencies of Salicornia and Atriplex, and broadest in spring, when the frequencies of these two plants were lowest. Diet breadth was slightly lower for RERA than for co‐occurring species in pairwise comparisons. All four species consumed similarly high frequencies of wetland plants, but RERA consumed fewer grasses and upland plants, suggesting that it may be less suited to fragmented habitat than sympatric rodents. Diet overlap was lowest between RERA and the native California vole (Microtis californicus). In contrast, RERA diet overlapped substantially with the native western harvest mouse (R. megalotis) and non‐native house mouse (Mus musculus), suggesting potential for competition if these species become sufficiently abundant.
Efficacy and tolerability of brivaracetam monotherapy in childhood and juvenile absence epilepsy: An innovative adaptive trial design
Authors: Bast Thomas , Schulz Anne‐Liv , Floricel Florin , Morita Diego , Cleveland Jody M. , Elshoff Jan‐Peer 
Published: July 2022

AbstractObjectiveDespite introduction of several antiseizure medications over the past two decades, treatment options for childhood absence epilepsy (CAE) and juvenile absence epilepsy (JAE) remain limited. We report the innovative adaptive design of an ongoing phase 2/3 trial to evaluate efficacy, safety, and tolerability of brivaracetam (BRV) monotherapy in patients 2–25 years of age with CAE or JAE.MethodsN01269 (ClinicalTrials.gov: NCT04666610; start: July 2021; expected completion: 2024) is a randomized, dose‐finding and confirmatory, double‐blind, placebo‐controlled, parallel‐group, multicenter trial. The trial consists of a dose‐selection and assessment for futility stage, followed by an optimal‐dose stage after interim analysis. Both stages include an up to 2‐week screening period, a 2‐week placebo‐controlled period, and an 11‐week active treatment period (10 weeks of initial treatment followed by a 24‐hour electroencephalogram [EEG] and an additional week of active treatment for 24‐hour EEG assessment). Patients who are absence seizure‐free will enter an up to 4‐week randomized withdrawal period. Efficacy assessments will be based on 24‐hour EEG and seizure diaries.SignificanceThis two‐stage adaptive trial design allows investigation of two potentially efficacious BRV doses, where one dose is dropped in favor of the other dose with a better benefit–risk profile. This allows for a combined phase 2 dose‐finding and phase 3 confirmatory efficacy trial, which reduces the number of patients needed to be recruited and reduces trial duration. A randomized withdrawal period is included to evaluate sustainability of treatment effect over time and to allow for placebo control while minimizing placebo exposure. Use of EEG capture in addition to seizure diaries offers a robust mechanism of detecting seizure activity and measuring treatment effect. Positive efficacy and safety/tolerability data may support the use of BRV as monotherapy for CAE or JAE, providing another treatment option and representing long‐delayed progress in the treatment of absence seizures in these populations.
Bringing life out of diversity: Boosting network lifetime using multi‐PHY routing in RPL
Authors: Rady Mina , Lampin Quentin , Barthel Dominique , Watteyne Thomas 
Published: July 2022

AbstractIn this article, we propose a routing mechanism based on the RPL protocol in a wireless network that is equipped with a mix of short‐range and long‐range radios. We introduce Life‐OF, an objective function for RPL which uses a combination of metrics and the diverse physical layers to boost the network's lifetime. We evaluate the performance of Life‐OF compared to the classical MRHOF objective function in simulations. Two key performance indicators (KPIs) are reported: network lifetime and network latency. Results demonstrate that MRHOF tends to converge to a pure long‐range network, leading to short network lifetime. However, Life‐OF improves network lifetime by continuously adapting the routing topology to favor routing over nodes with longest remaining lifetime. Life‐OF combines diverse radios and balances power consumption in the network. This way, nodes switch between using their short‐range radio to improve their own battery lifetime and using their long‐range radio to avoid routers that are close to depletion. Results show that using Life‐OF improves the lifetime of the network by up to 470% that of MRHOF, while maintaining similar latency.
Effect of vitamin C fortification on the quality of cow's and goat's yoghurt
Authors: Sobczak Alicja , Danowska‐Oziewicz Marzena , Ząbek Katarzyna , Miciński Jan , Narwojsz Agnieszka 
Published: July 2022

AbstractYoghurt is one of the well‐known fermented dairy products that play an important role in the human diet. At present, products made of goat's milk are becoming more popular. This study was conducted to evaluate the effect of physicochemical properties of yoghurt fortified with vitamin C. Six different yoghurts were developed: from goat's and cow's milk without any addition, with L‐ascorbic acid and acerola addition. The results showed that the addition of L‐ascorbic acid significantly decreased pH. Based on the sensory evaluation, the natural cow's yoghurt has scored higher in the overall rating among yoghurts. The addition of L‐ascorbic acid to natural goat's yoghurt positively affected the color, taste, flavor, and consistency. In the case of cow's milk yoghurt, the addition of L‐ascorbic acid and acerola deteriorated the taste of the product.
Effect of storage on the nutritional and antioxidant properties of brown Basmati rice
Authors: Naveed Aqsa , Zubair Muhammad , Baig Ayesha , Farid Mujahid , Ahmed Waqar , Rehman Rafia , Ayub Muhammad Adnan , Hassoun Abdo , Cropotova Janna 
Published: July 2022

AbstractThe purpose of the present study is to evaluate the effect of storage time and temperature on the nutritional and antioxidant values of different varieties of brown rice. PARB approved indigenous Basmati varieties (Basmati 86, Basmati 515, Basmati super, Basmati super fine and Basmati kainat) were procured and initially tested for physicochemical parameters, including moisture, ash, lipids, proteins, carbohydrates, and fibers from the brown rice powder. Similarly, antioxidant capacity of these brown rice samples was assessed in terms of total phenolic content and 2,2‐diphenyl‐1‐picrylhydrazyl radical‐scavenging potential. Samples of brown rice were stored for 3 and 6 months at 25 and 5°C. On increasing the storage time and temperature, antioxidant activity of rice decreases up to 50%. Nutritional parameters, such as minerals, carbohydrates, and fatty acids were characterized using UV/Vis spectrophotometer, ICP‐OES, GC–MS, and HPLC, revealing significant changes in the chemical composition of brown rice. Observation indicates that storage at high temperatures leads to a rapid decrease in carbohydrate and moisture content than at lower temperatures. The protein and ash content remains controlled and integrate with the mineral composition found. Decrease in the glucose and fructose amount was observed in brown rice varieties except for Basmati super fine and Basmati kainat at 5°C. Regarding fatty acids, oleic and linoleic acids were prominent in oils extracted from the different brown rice varieties, and their content was reduced during the storage due to conversion to behenic, and erucic acids, respectively. From the present study, it can be concluded that low storage temperatures reduce the loss of nutrients, offering better nutritional quality for the consumer.
Impacts of agar gum and fucoidan on gel properties of surimi products without phosphate
Authors: Zheng Mingjing , Hong Jinling , Chuai Pengjie , Chen Yanhong , Ni Hui , Li Qingbiao , Jiang Zedong 
Published: July 2022

AbstractPhosphate is widely used in surimi products to improve the gel properties. However, excess addition of phosphate occurs, which can harm the consumer's health. This study aimed to evaluate the effects of agar gum and fucoidan on maintaining the gel properties of surimi products instead of phosphate. Interestingly, our results showed that 0.125% of agar gum and fucoidan to replace phosphate could enhance water‐holding capacity and maintain gel strength and textual properties of surimi products well. Especially at frozen storage for 1 year, 0.125% of agar gum reduced the expressible moisture content of surimi products by around 10% (p < .05). Sensory evaluation showed that 0.125% of agar gum and fucoidan instead of phosphate can improve tissue and fondness of surimi products in refrigerated storage for 24 h but not in frozen storage for 1 year. The addition of agar gum and fucoidan at a high concentration >0.50% increased the WHC, but significantly decreased gel strength and springiness of surimi products (p < .05). Particularly, 1.00% of agar gum and fucoidan reduced gel strength by around 20% (p < .05). It might be due to the destruction of the gel network structure of surimi protein following the excess addition of these polysaccharides. It can be concluded that 0.125% of agar gum and fucoidan can replace phosphate to develop high‐quality surimi products, and excessive addition of them have negative effects.
Gut microbiome and metabolome analyses reveal the protective effect of special high‐docosahexaenoic acid tuna oil on d‐galactose‐induced aging in mice
Authors: Zhang Jing , Yi Congmin , Han Jiaojiao , Ming Tinghong , Zhou Jun , Lu Chenyang , Li Ye , Su Xiurong 
Published: July 2022

AbstractAging is closely related to altered gut function and its microbiome composition. To elucidate the mechanisms involved in the preventive effect of special high‐docosahexaenoic acid tuna oil (HDTO) on senescence, the effects of different doses of HDTO on the gut microbiome and metabolome of d‐galactose‐induced aging mice were studied. Deferribacteres and Tenericutes and uridine might be used as indicator bacteria and characteristic metabolites to identify aging, respectively. HDTO markedly improved the impaired memory and antioxidant abilities induced by d‐galactose. At the phylum level, the abundance of Firmicutes and Tenericutes was significantly increased upon d‐galactose induction, while that of Bacteroidetes, Proteobacteria, and Deferribacteres was significantly decreased. At the genus level, the variation mainly presented as an increase in the abundance of the Firmicutes genera Ligilactobacillus, Lactobacillus, and Erysipelothrix, the decrease in the abundance of the Bacteroidetes genera Bacteroides and Alistipes, the Firmicutes genus Dielma, and the Deferribacteres genus Mucispirillum. HDTO supplementation reversed the alterations in the intestinal flora by promoting the proliferation of beneficial flora during the aging process; the metabolic pathways, such as glycine–serine–threonine metabolism, valine–leucine–isoleucine biosynthesis, and some metabolic pathways involved in uridine, were also partially restored. Furthermore, the correlation analysis illustrated an obvious correlation between gut microbiota, its metabolites, and aging‐related indices. Moreover, it is worth noting that the metabolic regulation by dietary intervention varied with different HDTO doses and did not present a simple additive effect; indeed, each dose showed a unique modulation mechanism.