bluuebunny/crossref_metadata_2025 huggingface dataset:
Automated flow cytometry as a tool to obtain a fine-grain picture of marine prokaryote community structure along an entire oceanographic cruise
Authors: Pernice Massimo C. , Gasol Josep M.
Published: January 2023

On a standard oceanographic cruise, flow cytometry data are usually collected sparsely through a bottle-based sampling and with stations separated by kilometers leading to a fragmented view of the ecosystem; to improve the resolution of the datasets produced by this technique here it is proposed the application of an automatic method of sampling and staining. The system used consists of a flow-cytometer (Accuri-C6) connected to an automated continuous sampler (OC-300) that collects samples of marine surface waters every 15 min. We tested this system for five days during a brief Mediterranean cruise with the aim of estimating the abundance, relative size and phenotypic diversity of prokaryotes. Seawater was taken by a faucet linked to an inlet pump (ca. 5 m depth). Once the sample was taken, the Oncyt-300 stained it and sent it to the flow cytometer. A total of 366 samples were collected, effectively achieving a fine-grained scale view of microbial community composition both through space and time. A significative positive relationship was found comparing data obtained with the automatic method and 10 samples collected from the faucet but processed with the standard protocol. Abundance values retrieved varied from 3.56·105 cell mL−1 in the coastal area till 6.87 105 cell mL−1 in open waters, exceptional values were reached in the harbor area where abundances peaked to 1.28 106 cell mL−1. The measured features (abundance and size) were associated with metadata (temperature, salinity, conductivity) also taken in continuous, of which conductivity was the one that better explained the variability of abundance. A full 24 h measurement cycle was performed resulting in slightly higher median bacterial abundances values during daylight hours compared to night. Alpha diversity, calculated using computational cytometry techniques, showed a higher value in the coastal area above 41° of latitude and had a strong inverse relationship with both salinity and conductivity. This is the first time to our knowledge that the OC-300 is directly applied to the marine environment during an oceanographic cruise; due to its high-resolution, this set-up shows great potential both to cover large sampling areas, and to monitor day-night cycles in situ.
Fungi and cercozoa regulate methane-associated prokaryotes in wetland methane emissions
Authors: Wang Linlin , Zhao Mingliang , Du Xiongfeng , Feng Kai , Gu Songsong , Zhou Yuqi , Yang Xingsheng , Zhang Zhaojing , Wang Yingcheng , Zhang Zheng , Zhang Qi , Xie Baohua , Han Guangxuan , Deng Ye
Published: January 2023

Wetlands are natural sources of methane (CH4) emissions, providing the largest contribution to the atmospheric CH4 pool. Changes in the ecohydrological environment of coastal salt marshes, especially the surface inundation level, cause instability in the CH4 emission levels of coastal ecosystems. Although soil methane-associated microorganisms play key roles in both CH4 generation and metabolism, how other microorganisms regulate methane emission and their responses to inundation has not been investigated. Here, we studied the responses of prokaryotic, fungal and cercozoan communities following 5 years of inundation treatments in a wetland experimental site, and molecular ecological networks analysis (MENs) was constructed to characterize the interdomain relationship. The result showed that the degree of inundation significantly altered the CH4 emissions, and the abundance of the pmoA gene for methanotrophs shifted more significantly than the mcrA gene for methanogens, and they both showed significant positive correlations to methane flux. Additionally, we found inundation significantly altered the diversity of the prokaryotic and fungal communities, as well as the composition of key species in interactions within prokaryotic, fungal, and cercozoan communities. Mantel tests indicated that the structure of the three communities showed significant correlations to methane emissions (p < 0.05), suggesting that all three microbial communities directly or indirectly contributed to the methane emissions of this ecosystem. Correspondingly, the interdomain networks among microbial communities revealed that methane-associated prokaryotic and cercozoan OTUs were all keystone taxa. Methane-associated OTUs were more likely to interact in pairs and correlated negatively with the fungal and cercozoan communities. In addition, the modules significantly positively correlated with methane flux were affected by environmental stress (i.e., pH) and soil nutrients (i.e., total nitrogen, total phosphorus and organic matter), suggesting that these factors tend to positively regulate methane flux by regulating microbial relationships under inundation. Our findings demonstrated that the inundation altered microbial communities in coastal wetlands, and the fungal and cercozoan communities played vital roles in regulating methane emission through microbial interactions with the methane-associated community.
Comparative genomics reveals cellobiose hydrolysis mechanism of Ruminiclostridium thermocellum M3, a cellulosic saccharification bacterium
Authors: Tao Sheng , Qingbin Meng , Zhiling Li , Caiyu Sun , Lixin Li , Lilai Liu
Published: January 2023

The cellulosome of Ruminiclostridium thermocellum was one of the most efficient cellulase systems in nature. However, the product of cellulose degradation by R. thermocellum is cellobiose, which leads to the feedback inhibition of cellulosome, and it limits the R. thermocellum application in the field of cellulosic biomass consolidated bioprocessing (CBP) industry. In a previous study, R. thermocellum M3, which can hydrolyze cellulosic feedstocks into monosaccharides, was isolated from horse manure. In this study, the complete genome of R. thermocellum M3 was sequenced and assembled. The genome of R. thermocellum M3 was compared with the other R. thermocellum to reveal the mechanism of cellulosic saccharification by R. thermocellum M3. In addition, we predicted the key genes for the elimination of feedback inhibition of cellobiose in R. thermocellum. The results indicated that the whole genome sequence of R. thermocellum M3 consisted of 3.6 Mb of chromosomes with a 38.9% of GC%. To be specific, eight gene islands and 271 carbohydrate-active enzyme-encoded proteins were detected. Moreover, the results of gene function annotation showed that 2,071, 2,120, and 1,246 genes were annotated into the Clusters of Orthologous Groups (COG), Gene Ontology (GO), and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases, respectively, and most of the genes were involved in carbohydrate metabolism and enzymatic catalysis. Different from other R. thermocellum, strain M3 has three proteins related to β-glucosidase, and the cellobiose hydrolysis was enhanced by the synergy of gene BglA and BglX. Meanwhile, the GH42 family, CBM36 family, and AA8 family might participate in cellobiose degradation.
A culture-, amplification-independent, and rapid method for identification of pathogens and antibiotic resistance profile in bovine mastitis milk
Authors: Ahmadi Asal , Khezri Abdolrahman , Nørstebø Håvard , Ahmad Rafi
Published: January 2023

Introduction

Rapid and accurate diagnosis of causative pathogens in mastitis would minimize the imprudent use of antibiotics and, therefore, reduce the spread of antimicrobial resistance. Whole genome sequencing offers a unique opportunity to study the microbial community and antimicrobial resistance (AMR) in mastitis. However, the complexity of milk samples and the presence of a high amount of host DNA in milk from infected udders often make this very challenging.

Methods

Here, we tested 24 bovine milk samples (18 mastitis and six non-mastitis) using four different commercial kits (Qiagens’ DNeasy® PowerFood® Microbial, Norgens’ Milk Bacterial DNA Isolation, and Molzyms’ MolYsis™ Plus and Complete5) in combination with filtration, low-speed centrifugation, nuclease, and 10% bile extract of male bovine (Ox bile). Isolated DNA was quantified, checked for the presence/absence of host and pathogen using PCR and sequenced using MinION nanopore sequencing. Bioinformatics analysis was performed for taxonomic classification and antimicrobial resistance gene detection.

Results

The results showed that kits designed explicitly for bacterial DNA isolation from food and dairy matrices could not deplete/minimize host DNA. Following using MolYsis™ Complete 5 + 10% Ox bile + micrococcal nuclease combination, on average, 17% and 66.5% of reads were classified as bovine and Staphylococcus aureus reads, respectively. This combination also effectively enriched other mastitis pathogens, including Escherichia coli and Streptococcus dysgalactiae. Furthermore, using this approach, we identified important AMR genes such as Tet (A), Tet (38), fosB-Saur, and blaZ. We showed that even 40 min of the MinION run was enough for bacterial identification and detecting the first AMR gene.

Conclusion

We implemented an effective method (sensitivity of 100% and specificity of 92.3%) for host DNA removal and bacterial DNA enrichment (both gram-negative and positive) directly from bovine mastitis milk. To the best of our knowledge, this is the first culture- and amplification-independent study using nanopore-based metagenomic sequencing for real-time detection of the pathogen (within 5 hours) and the AMR profile (within 5–9 hours), in mastitis milk samples. These results provide a promising and potential future on-farm adaptable approach for better clinical management of mastitis.
Microbial membrane lipid adaptations to high hydrostatic pressure in the marine environment
Authors: Tamby Anandi , Sinninghe Damsté Jaap S. , Villanueva Laura
Published: January 2023

The deep-sea is characterized by extreme conditions, such as high hydrostatic pressure (HHP) and near-freezing temperature. Piezophiles, microorganisms adapted to high pressure, have developed key strategies to maintain the integrity of their lipid membrane at these conditions. The abundance of specific membrane lipids, such as those containing unsaturated and branched-chain fatty acids, rises with increasing HHP. Nevertheless, this strategy is not universal among piezophiles, highlighting the need to further understand the effects of HHP on microbial lipid membranes. Challenges in the study of lipid membrane adaptations by piezophiles also involve methodological developments, cross-adaptation studies, and insight into slow-growing piezophiles. Moreover, the effects of HHP on piezophiles are often difficult to disentangle from effects caused by low temperature that are often characteristic of the deep sea. Here, we review the knowledge of membrane lipid adaptation strategies of piezophiles, and put it into the perspective of marine systems, highlighting the future challenges of research studying the effects of HHP on the microbial lipid composition.
A direct nuclear magnetic resonance method to investigate lysine acetylation of intrinsically disordered proteins
Authors: Fraser Olivia A. , Dewing Sophia M. , Usher Emery T. , George Christy , Showalter Scott A.
Published: January 2023

Intrinsically disordered proteins are frequent targets for functional regulation through post-translational modification due to their high accessibility to modifying enzymes and the strong influence of changes in primary structure on their chemical properties. While lysine Nε-acetylation was first observed as a common modification of histone tails, proteomic data suggest that lysine acetylation is ubiquitous among both nuclear and cytosolic proteins. However, compared with our biophysical understanding of the other common post-translational modifications, mechanistic studies to document how lysine Nε-acetyl marks are placed, utilized to transduce signals, and eliminated when signals need to be turned off, have not kept pace with proteomic discoveries. Herein we report a nuclear magnetic resonance method to monitor Nε-lysine acetylation through enzymatic installation of a13C-acetyl probe on a protein substrate, followed by detection through 13C direct-detect spectroscopy. We demonstrate the ease and utility of this method using histone H3 tail acetylation as a model. The clearest advantage to this method is that it requires no exogenous tags that would otherwise add steric bulk, change the chemical properties of the modified lysine, or generally interfere with downstream biochemical processes. The non-perturbing nature of this tagging method is beneficial for application in any system where changes to local structure and chemical properties beyond those imparted by lysine modification are unacceptable, including intrinsically disordered proteins, bromodomain containing protein complexes, and lysine deacetylase enzyme assays.
Evaluation of AQP4 functional variants and its association with fragile X-associated tremor/ataxia syndrome
Authors: Elias-Mas Andrea , Potrony Miriam , Bague Jaume , Cutler David J. , Alvarez-Mora Maria Isabel , Torres Teresa , Barcos Tamara , Puig-Butille Joan Anton , Rubio Marta , Madrigal Irene , Puig Susana , Allen Emily G. , Rodriguez-Revenga Laia
Published: January 2023

Introduction

Fragile X-associated tremor/ataxia syndrome (FXTAS, OMIM# 300623) is a late-onset neurodegenerative disorder with reduced penetrance that appears in adult FMR1 premutation carriers (55–200 CGGs). Clinical symptoms in FXTAS patients usually begin with an action tremor. After that, different findings including ataxia, and more variably, loss of sensation in the distal lower extremities and autonomic dysfunction, may occur, and gradually progress. Cognitive deficits are also observed, and include memory problems and executive function deficits, with a gradual progression to dementia in some individuals. Aquaporin 4 (AQP4) is a commonly distributed water channel in astrocytes of the central nervous system. Changes in AQP4 activity and expression have been implicated in several central nervous system disorders. Previous studies have suggested the associations of AQP4 single nucleotide polymorphisms (SNPs) with brain-water homeostasis, and neurodegeneration disease. To date, this association has not been studied in FXTAS.

Methods

To investigate the association of AQP4 SNPs with the risk of presenting FXTAS, a total of seven common AQP4 SNPs were selected and genotyped in 95 FMR1 premutation carriers with FXTAS and in 65 FMR1 premutation carriers without FXTAS.

Results

The frequency of AQP4-haplotype was compared between groups, denoting 26 heterozygous individuals and 5 homozygotes as carriers of the minor allele in the FXTAS group and 25 heterozygous and 2 homozygotes in the no-FXTAS group. Statistical analyses showed no significant associations between AQP4 SNPs/haplotypes and development of FXTAS.

Discussion

Although AQP4 has been implicated in a wide range of brain disorders, its involvement in FXTAS remains unclear. The identification of novel genetic markers predisposing to FXTAS or modulating disease progression is critical for future research involving predictors and treatments.
α2-Adrenergic modulation of Ih in adult-born granule cells in the olfactory bulb
Authors: Hu Ruilong , Shankar Janam , Dong Grant Z. , Villar Pablo S. , Araneda Ricardo C.
Published: January 2023

In the olfactory bulb (OB), a large population of axon-less inhibitory interneurons, the granule cells (GCs), coordinate network activity and tune the output of principal neurons, the mitral and tufted cells (MCs), through dendrodendritic interactions. Furthermore, GCs undergo neurogenesis throughout life, providing a source of plasticity to the neural network of the OB. The function and integration of GCs in the OB are regulated by several afferent neuromodulatory signals, including noradrenaline (NA), a state-dependent neuromodulator that plays a crucial role in the regulation of cortical function and task-specific decision processes. However, the mechanisms by which NA regulates GC function are not fully understood. Here, we show that NA modulates hyperpolarization-activated currents (Ih) via the activation of α2-adrenergic receptors (ARs) in adult-born GCs (abGCs), thus directly acting on channels that play essential roles in regulating neuronal excitability and network oscillations in the brain. This modulation affects the dendrodendritic output of GCs leading to an enhancement of lateral inhibition onto the MCs. Furthermore, we show that NA modulates subthreshold resonance in GCs, which could affect the temporal integration of abGCs. Together, these results provide a novel mechanism by which a state-dependent neuromodulator acting on Ih can regulate GC function in the OB.
Burning the candle at both ends: Intraretinal signaling of intrinsically photosensitive retinal ganglion cells
Authors: Raja Sushmitha , Milosavljevic Nina , Allen Annette E. , Cameron Morven A.
Published: January 2023

Intrinsically photosensitive retinal ganglion cells (ipRGCs) are photoreceptors located in the ganglion cell layer. They project to brain regions involved in predominately non-image-forming functions including entrainment of circadian rhythms, control of the pupil light reflex, and modulation of mood and behavior. In addition to possessing intrinsic photosensitivity via the photopigment melanopsin, these cells receive inputs originating in rods and cones. While most research in the last two decades has focused on the downstream influence of ipRGC signaling, recent studies have shown that ipRGCs also act retrogradely within the retina itself as intraretinal signaling neurons. In this article, we review studies examining intraretinal and, in addition, intraocular signaling pathways of ipRGCs. Through these pathways, ipRGCs regulate inner and outer retinal circuitry through both chemical and electrical synapses, modulate the outputs of ganglion cells (both ipRGCs and non-ipRGCs), and influence arrangement of the correct retinal circuitry and vasculature during development. These data suggest that ipRGC function plays a significant role in the processing of image-forming vision at its earliest stage, positioning these photoreceptors to exert a vital role in perceptual vision. This research will have important implications for lighting design to optimize the best chromatic lighting environments for humans, both in adults and potentially even during fetal and postnatal development. Further studies into these unique ipRGC signaling pathways could also lead to a better understanding of the development of ocular dysfunctions such as myopia.
Language reorganization patterns in global aphasia–evidence from fNIRS
Authors: Li Haozheng , Liu Jianju , Tian Shan , Fan Shunjuan , Wang Tingwei , Qian Hong , Liu Gang , Zhu Yulian , Wu Yi , Hu Ruiping
Published: January 2023

Background

Exploring the brain reorganization patterns associated with language recovery would promote the treatment of global aphasia. While functional near-infrared spectroscopy (fNIRS) has been widely used in the study of speech and language impairment, its application in the field of global aphasia is still limited.

Aims

We aimed to identify cortical activation patterns of patients with global aphasia during naming and repetition tasks.

Methods and procedures

We recruited patients with post-stroke aphasia from the Department of Rehabilitation Medicine at Huashan Hospital. These individuals were diagnosed with global aphasia without cognitive impairments, as assessed by speech-language pathology evaluations. Age- and sex-matched healthy controls were recruited from the greater Shanghai area. During fNIRS measurement, patients and healthy controls completed the picture-naming and phrase repetition task. Cortical activation patterns on each of these language tasks were then compared between groups.

Outcomes and results

A total of nine patients with global aphasia and 14 healthy controls were included in this study. Compared with the healthy subjects, patients with global aphasia showed increased activation in the left Broca's area, middle temporal gyrus (MTG), superior temporal gyrus (STG), and pre-motor and supplementary motor cortex (SMA) (p < 0.05) in the picture-naming task. Furthermore, the latency of the oxyhemoglobin (HbO) concentration in the left supramarginal gyrus (SMG) region had a strong negative correlation with their score of the naming task (p < 0.01). In the phrase repetition task, decreased activation was detected in the left SMA and SMG (p < 0.05) of patients relative to controls.

Conclusion

The left SMG plays a critical role in the language function of patients with global aphasia, especially in their abilities to name and repeat. fNIRS is a promising approach to revealing the changes in brain activities in patients with aphasia, and we believe it will contribute to a deeper understanding of the neurological mechanisms and the establishment of a novel treatment approach for global aphasia.
Mitochondrial encephalomyopathy with lactic acidosis and stroke-like episodes with an MT-TL1 m.3243A>G point mutation: Neuroradiological features and their implications for underlying pathogenesis
Authors: Zheng Helin , Zhang Xuemei , Tian Lu , Liu Bo , He Xiaoya , Wang Longlun , Ding Shuang , Guo Yi , Cai Jinhua
Published: January 2023

Objective

Mitochondrial encephalomyopathy with lactic acidosis and stroke−like episodes (MELAS) is one of the most common inherited mitochondrial disorders. Due to the high clinical and genetic heterogeneity of MELAS, it is still a major challenge for clinicians to accurately diagnose the disease at an early stage. Herein, we evaluated the neuroimaging findings of MELAS with an m.3243A>G mutation in MT−TL1 and analyzed the possible underlying pathogenesis of stroke-like episodes.

Materials and methods

Fifty-nine imaging studies in 24 patients who had a confirmed genetic diagnosis of m.3243A>G (MT-TL1; tRNALeu) associated with MELAS were reviewed in our case series. The anatomic location, morphological features, signal/intensity characteristics and temporal evolution of lesions were analyzed on magnetic resonance imaging (MRI), and computed tomography (CT) images. The supplying vessels and metabolite content of the lesions were also evaluated by using MR angiography (MRA)/CT angiography (CTA), and MR spectroscopy (MRS), respectively.

Results

The lesions were most commonly located in the posterior brain, with 37 (37/59, 63%) in the occipital lobe, 32 (32/59, 54%) in the parietal lobe, and 30 (30/59, 51%) in the temporal lobe. The signal characteristics of the lesions varied and evolved over time. Bilateral basal ganglia calcifications were found in 6 of 9 (67%) patients who underwent CT. Cerebral and cerebellar atrophy were found in 38/59 (64%) and 40/59 (68%) patients, respectively. Lesion polymorphism was found in 37/59 (63%) studies. MRS showed elevated lactate doublet peaks in 9/10 (90%) cases. MRA or CTA revealed that the lesion-related arteries were slightly dilated compared with those of the contralateral side in 4 of 6 (67%) cases.

Conclusion

The imaging features of MELAS vary depending on the disease stage. Polymorphic lesions in a single imaging examination should be considered a diagnostic clue for MELAS. Stroke-like episodes may be involved in a complex pathogenetic process, including mitochondrial angiopathy, mitochondrial cytopathy, and neuronal excitotoxicity.
Alterations in brain structure and function associated with pediatric growth hormone deficiency: A multi-modal magnetic resonance imaging study
Authors: Zhou Zhibo , Luo Yunyun , Gao Xiaoxing , Zhu Yanlin , Bai Xi , Yang Hongbo , Bi Qiuhui , Chen Shi , Duan Lian , Wang Linjie , Gong Fengying , Feng Feng , Gong Gaolang , Zhu Huijuan , Pan Hui
Published: January 2023

Introduction

Pediatric growth hormone deficiency (GHD) is a disease resulting from impaired growth hormone/insulin-like growth factor-1 (IGF-1) axis but the effects of GHD on children’s cognitive function, brain structure and brain function were not yet fully illustrated.

Methods

Full Wechsler Intelligence Scales for Children, structural imaging, diffusion tensor imaging, and resting-state functional magnetic resonance imaging were assessed in 11 children with GHD and 10 matched healthy controls.

Results

(1) The GHD group showed moderate cognitive impairment, and a positive correlation existed between IGF-1 levels and cognitive indices. (2) Mean diffusivity was significantly increased in both corticospinal tracts in GHD group. (3) There were significant positive correlations between IGF-1 levels and volume metrics of left thalamus, left pallidum and right putamen but a negative correlation between IGF-1 levels and cortical thickness of the occipital lobe. And IGF-1 levels negatively correlated with fractional anisotropy in the superior longitudinal fasciculus and right corticospinal tract. (4) Regional homogeneity (ReHo) in the left hippocampus/parahippocampal gyrus was negatively correlated with IGF-1 levels; the amplitude of low-frequency fluctuation (ALFF) and ReHo in the paracentral lobe, postcentral gyrus and precentral gyrus were also negatively correlated with IGF-1 levels, in which region ALFF fully mediates the effect of IGF-1 on working memory index.

Conclusion

Multiple subcortical, cortical structures, and regional neural activities might be influenced by serum IGF-1 levels. Thereinto, ALFF in the paracentral lobe, postcentral gyrus and precentral gyrus fully mediates the effect of IGF-1 on the working memory index.
New prospects on cerebellar reserve: Remarks on neuroprotective effects of experience in animals and humans
Authors: Gelfo Francesca , Serra Laura , Petrosini Laura
Published: January 2023

The ability of the brain to change structure and function in response to experience accounts for its ability to successfully adapt to the environment in both learning processes and unique phases, such as during development and repair. On this basis, the occurrence of the brain, cognitive, and neural reserves has been advanced to explain the discrepancies between the extent of neurological damage and the severity of clinical manifestations described in patients with different life span experiences. Research on this topic highlighted the neuroprotective role of complex stimulations, allowing the brain to better cope with the damage. This framework was initially developed by observing patients with Alzheimer's disease, and it has since been progressively expanded to multifarious pathological states. The cerebellum is known to be particularly responsive to experience through extensive plastic rearrangements. The neuroprotective value exerted by reserve mechanisms appears to be suitable for basic neuronal plasticity in the cerebellum. Thus, it is of primary interest to deepen our understanding of how life experiences modify individuals' cerebellar morphology and functionality. The present study is aimed at analyzing the evidence provided on this topic by animal and human studies. For animals, we considered the studies in which subjects were submitted to enhanced stimulations before the damage occurred. For humans, we considered studies in which previous lifelong high-level experiences were associated with superior cerebellar abilities to cope with injury. Detailed indications of the processes underlying cerebellar reserves may be important in proposing effective interventions for patients suffering from pathologies that directly or indirectly damage cerebellar functionality.
Response surface optimization of light conditions for organic matter accumulation in two different shapes of Arthrospira platensis
Authors: Jian-Fei Sun , Meng-hui Shang , Xiao-nan Zang
Published: January 2023

Arthrospira platensis has attracted wide attention as a cyanobacteria with high nutritional value. In this research, the response surface method was used to study the effects of light cycle, light intensity and red-blue LED conditions on the growth and organic matter accumulation in spiral shaped strain A. platensis OUC623 and linear shaped strain A. platensis OUC793. The light conditions suitable for A. platensis OUC623 were as follows: growth (light time 12.01 h, light intensity 35.64 μmol/m2s, LED red: blue = 6.38:1); chlorophyll a (light time 12.75 h, light intensity 31.06 μmol/m2s, red: blue = 6.25:1); carotenoid (light time 13.12 h, light intensity 32.25 μmol/m2s, red: blue = 5.79:1); polysaccharide (light time 16.00 h, light intensity 31.32 μmol/m2s, blue: red = 6.24:1); protein (light time 12.18 h, light intensity 6.12 μmol/m2s, blue: red = 7.95:1); phycocyanin (light time12.00 h, light intensity 5.00 μmol/m2s, blue: red = 8.00:1). The light conditions suitable for A. platensis OUC793 were as follows: growth (light time 13.52 h, light intensity 40.22 μmol/m2s, red: blue = 5.98:1); chlorophyll a (light time 14.22 h, light intensity 44.96 μmol/m2s, red: blue = 5.94:1); carotenoid (light time 14.13 h, light intensity 44.50 μmol/m2s, red: blue = 6.02:1); polysaccharide (light time 16.00 h, light intensity 31.85 μmol/m2s, blue: red = 6.08:1); protein (light time12.00 h, light intensity 5.00 μmol/m2s, blue: red = 8.00:1); phycocyanin (light time12.01 h, light intensity 5.01 μmol/m2s, blue: red = 8.00:1). Under the theoretical optimal light conditions, compared with white LED, the growth rate, chlorophyll a, carotenoid, phycocyanin, protein and polysaccharide contents in strain 623 increased by 91.67%, 114.70%, 85.05%, 563.54%, 386.14%, 201.18%, and in strain 793 increased by 75.00%, 150.94%, 113.43%, 427.09%, 1284.71%, 312.38%, respectively. The two strains showed different advantages. Growth rate, chlorophyll a, polysaccharide, protein and phycocyanin content of strain 623 were higher than those of strain 793, while carotenoid was higher in strain 793. After optimization, both strains could reach a good growth state, and the growth rate and organic matter content were close. And then a 20 L photobioreactor was used to expand the culture of the two strains, validating the theoretical optimal light conditions of response surface method. This study laid the foundation for the establishment of optical conditions for organic matter accumulation in two different strains of A. platensis, which provided more options for meeting the industrialization needs of A. platensis.
Multitasking dynamic contrast enhanced magnetic resonance imaging can accurately differentiate chronic pancreatitis from pancreatic ductal adenocarcinoma
Authors: Wang Nan , Gaddam Srinivas , Xie Yibin , Christodoulou Anthony G. , Wu Chaowei , Ma Sen , Fan Zhaoyang , Wang Lixia , Lo Simon , Hendifar Andrew E. , Pandol Stephen J. , Li Debiao
Published: January 2023

Background and aims

Accurate differentiation of chronic pancreatitis (CP) and pancreatic ductal adenocarcinoma (PDAC) is an area of unmet clinical need. In this study, a novel Multitasking dynamic contrast enhanced (DCE) magnetic resonance imaging (MRI) technique was used to quantitatively evaluate the microcirculation properties of pancreas in CP and PDAC and differentiate between them.

Methods

The Multitasking DCE technique was able to acquire one 3D image per second during the passage of MRI contrast agent, allowing the quantitative estimation of microcirculation properties of tissue, including blood flow Fp, plasma volume fraction vp, transfer constant Ktrans, and extravascular extracellular volume fraction ve. Receiver operating characteristic (ROC) analysis was performed to differentiate the CP pancreas, PDAC pancreas, normal control pancreas, PDAC tumor, PDAC upstream, and PDAC downstream. ROCs from quantitative analysis and conventional analysis were compared.

Results

Fourteen PDAC patients, 8 CP patients and 20 healthy subjects were prospectively recruited. The combination of Fp, vp, Ktrans, and ve can differentiate CP versus PDAC pancreas with good AUC (AUC [95% CI] = 0.821 [0.654 – 0.988]), CP versus normal pancreas with excellent AUC (1.000 [1.000 – 1.000]), PDAC pancreas versus normal pancreas with excellent AUC (1.000 [1.000 – 1.000]), CP versus PDAC tumor with excellent AUC (1.000 [1.000 – 1.000]), CP versus PDAC downstream with excellent AUC (0.917 [0.795 – 1.000]), and CP versus PDAC upstream with fair AUC (0.722 [0.465 – 0.980]). This quantitative analysis outperformed conventional analysis in differentiation of each pair.

Conclusion

Multitasking DCE MRI is a promising clinical tool that is capable of unbiased quantitative differentiation between CP from PDAC.
Inhibition of RNF182 mediated by Bap promotes non-small cell lung cancer progression
Authors: Liu Yating , Ouyang Lianlian , Mao Chao , Chen Yuanbing , Liu Na , Chen Ling , Shi Ying , Xiao Desheng , Liu Shuang , Tao Yongguang
Published: January 2023

Introduction

Ubiquitylation that mediated by ubiquitin ligases plays multiple roles not only in proteasome-mediated protein degradation but also in various cellular process including DNA repair, signal transduction and endocytosis. RING finger (RNF) proteins form the majority of these ubiquitin ligases. Recent studies have demonstrated the important roles of RNF finger proteins in tumorigenesis and tumor progression. Benzo[a]pyrene (BaP) is one of the most common environmental carcinogens causing lung cancer. The molecular mechanism of Bap carcinogenesis remains elusive. Considering the critical roles of RNF proteins in tumorigenesis and tumor progression, we speculate on whether Bap regulates RNF proteins resulting in carcinogenesis.

Methods

We used GEO analysis to identify the potential RING finger protein family member that contributes to Bap-induced NSCLC. We next used RT-qPCR, Western blot and ChIP assay to investigate the potential mechanism of Bap inhibits RNF182. BGS analyses were used to analyze the methylation level of RNF182.

Results

Here we reported that the carcinogen Bap suppresses the expression of ring finger protein 182 (RNF182) in non-small cell lung cancer (NSCLC) cells, which is mediated by abnormal hypermethylation in an AhR independent way and transcriptional regulation in an AhR dependent way. Furthermore, RNF182 exhibits low expression and hypermethylation in tumor tissues. RNF182 also significantly suppresses cell proliferation and induces cell cycle arrest in NSCLC cell lines.

Conclusion

These results demonstrated that Bap inhibits RNF182 expression to promote lung cancer tumorigenesis through activating AhR and promoting abnormal methylation.
Diagnostic value of multiple ultrasound diagnostic techniques for axillary lymph node metastases in breast cancer: A systematic analysis and network meta-analysis
Authors: Li Jun , Wang Si-Rui , Li Qiao-Li , Zhu Tong , Zhu Pei-Shan , Chen Ming , Cui Xin-Wu
Published: January 2023

Background

Early diagnosis of axillary lymph node metastasis is very important for the recurrence and prognosis of breast cancer. Currently, Lymph node biopsy is one of the important methods to detect lymph node metastasis in breast cancer, however, its invasiveness might bring complications to patients. Therefore, this study investigated the diagnostic performance of multiple ultrasound diagnostic methods for axillary lymph node metastasis of breast cancer.

Materials and methods

In this study, we searched PubMed, Web of Science, CNKI and Wan Fang databases, conducted Bayesian network meta-analysis (NMA) on the studies that met the inclusion criteria, and evaluated the consistency of five different ultrasound imaging techniques in axillary lymph node metastasis of breast cancer. Funnel graph was used to evaluate whether it had publication bias. The diagnostic performance of each ultrasound imaging method was ranked using SUCRA

Results

A total of 22 papers were included, US+CEUS showed the highest SUCRA values in terms of sensitivity (SEN) (0.874), specificity (SPE) (0.911), positive predictive value (PPV) (0.972), negative predictive value (NPV) (0.872) and accuracy (ACC) (0.990).

Conclusion

In axillary lymph node metastasis of breast cancer, the US+CEUS combined diagnostic method showed the highest SUCRA value among the five ultrasound diagnostic methods. This study provides a theoretical basis for preoperative noninvasive evaluation of axillary lymph node metastases in breast cancer patients and clinical treatment decisions.

Systematic review registration

https://www.crd.york.ac.uk/PROSPERO/, identifier CRD42022351977.
Quantitative tissue proteome profile reveals neutrophil degranulation and remodeling of extracellular matrix proteins in early stage gallbladder cancer
Authors: Akhtar Javed , Jain Vaishali , Kansal Radhika , Priya Ratna , Sakhuja Puja , Goyal Surbhi , Agarwal Anil Kumar , Ghose Vivek , Polisetty Ravindra Varma , Sirdeshmukh Ravi , Kar Sudeshna , Gautam Poonam
Published: January 2023

Gallbladder cancer (GBC) is an aggressive malignancy of the gastrointestinal tract with a poor prognosis. It is important to understand the molecular processes associated with the pathogenesis of early stage GBC and identify proteins useful for diagnostic and therapeutic strategies. Here, we have carried out an iTRAQ-based quantitative proteomic analysis of tumor tissues from early stage GBC cases (stage I, n=7 and stage II, n=5) and non-tumor controls (n=6) from gallstone disease (GSD). We identified 357 differentially expressed proteins (DEPs) based on ≥ 2 unique peptides and ≥ 2 fold change with p value < 0.05. Pathway analysis using the STRING database showed, ‘neutrophil degranulation’ to be the major upregulated pathway that includes proteins such as MPO, PRTN3, S100A8, MMP9, DEFA1, AZU, and ‘ECM organization’ to be the major downregulated pathway that includes proteins such as COL14A1, COL1A2, COL6A1, COL6A2, COL6A3, BGN, DCN. Western blot and/or IHC analysis confirmed the elevated expression of MPO, PRTN3 and S100A8 in early stage of the disease. Based on the above results, we hypothesize that there is an increased neutrophil infiltration in tumor tissue and neutrophil degranulation leading to degradation of extracellular matrix (ECM) proteins promoting cancer cell invasion in the early stage GBC. Some of the proteins (MPO, MMP9, DEFA1) associated with ‘neutrophil degranulation’ showed the presence of ‘signal sequence’ suggesting their potential as circulatory markers for early detection of GBC. Overall, the study presents a protein dataset associated with early stage GBC.
KIF5A upregulation in hepatocellular carcinoma: A novel prognostic biomarker associated with unique tumor microenvironment status
Authors: Liu Qi , Liu Yu-yang , Chen Xue-min , Tao Bing-yan , Chen Kuang , Li Wei-min , Xu Chang-tao , Shi Ying , Li Hao , Liu Hao-run
Published: January 2023

Liver hepatocellular carcinoma (LIHC) is one of the most common liver malignancies with high mortality and morbidity. Thus, it is crucial to identify potential biomarker that is capable of accurately predicting the prognosis and therapeutic response of LIHC. Kinesin family member 5A (KIF5A) is a microtubule-based motor protein involved in the transport of macromolecules such as organelle proteins in cells. Recent studies have illustrated that the high expression of KIF5A was related to poor prognosis of solid tumors, including bladder cancer, prostate cancer, and breast cancer. However, little is currently known concerning the clinical significance of KIF5A expression in LIHC. Herein, by adopting multi-omics bioinformatics analysis, we comprehensively uncovered the potential function and the predictive value of KIF5A in stratifying clinical features among patients with LIHC, for which a high KIF5A level predicted an unfavorable clinical outcome. Results from KIF5A-related network and enrichment analyses illustrated that KIF5A might involve in microtubule-based process, antigen processing and presentation of exogenous peptide antigen via MHC class II. Furthermore, immune infiltration and immune function analyses revealed upregulated KIF5A could predict a unique tumor microenvironment with more CD8+T cells and a higher level of anti-tumor immune response. Evidence provided by immunohistochemistry staining (IHC) further validated our findings at the protein level. Taken together, KIF5A might serve as a novel prognostic biomarker for predicting immunotherapy response and could be a potential target for anti-cancer strategies for LIHC.
Case report: Imaging findings of true thymic hyperplasia at 18F-FDG PET/CT in an infant
Authors: Ren Jiazhong , Fu Zheng , Zhao Yaqing
Published: January 2023

True thymic hyperplasia (TTH) in children is rare and difficult to distinguish from other thymic tumors such as thymoma and thymic carcinoma. A 3‐year‐old girl underwent an 18F‐fluorodeoxyglucose (18F‐FDG) positron emission tomography (PET)/computed tomography (CT) scan (18F‐FDG PET/CT) and a chest CT scan to evaluate an anterior mediastinal mass. 18F‐FDG PET/CT revealed a mediastinal mass showing heterogeneously increased FDG uptake with a maximum standardized uptake value (SUVmax) of 7.1. Eventually, postoperative pathological diagnosis demonstrated TTH. So far, there are no reports of 18F‐FDG PET/CT imaging of this disease.
Systemic treatments for breast cancer brain metastasis
Authors: Chen Qiuchi , Xiong Jie , Ma Yuxi , Wei Jielin , Liu Cuiwei , Zhao Yanxia
Published: January 2023

Breast cancer (BC) is the most common cancer in females and BC brain metastasis (BCBM) is considered as the second most frequent brain metastasis. Although the advanced treatment has significantly prolonged the survival in BC patients, the prognosis of BCBM is still poor. The management of BCBM remains challenging. Systemic treatments are important to maintain control of central nervous system disease and improve patients’ survival. BCBM medical treatment is a rapidly advancing area of research. With the emergence of new targeted drugs, more options are provided for the treatment of BM. This review features currently available BCBM treatment strategies and outlines novel drugs and ongoing clinical trials that may be available in the future. These treatment strategies are discovered to be more efficacious and potent, and present a paradigm shift in the management of BCBMs.
The (Sialyl) Tn antigen: Contributions to immunosuppression in gastrointestinal cancers
Authors: Rajesh Christabelle , Radhakrishnan Prakash
Published: January 2023

Cellular signaling pathways are intricately regulated to maintain homeostasis. During cancer progression, these mechanisms are manipulated to become harmful. O-glycosylation, a crucial post-translational modification, is one such pathway that can lead to multiple isoforms of glycoproteins. The Tn (GalNAc-O-Ser/Thr) and Sialyl Tn (STn; Neu5Ac-GalNAc-O-Ser/Thr) antigens resulting from the incomplete synthesis of fully branched O-glycan chains on proteins contribute to disease progression in the pancreas and other gastrointestinal cancers. The tumor microenvironment (TME) is a major constituent of tumors and a key modulator of their behavior. Multiple cellular and secretory components of the TME dictate the development and metastasis of tumors. Immune cells like macrophages, natural killer (NK) cells, dendritic cells, B and T lymphocytes are a part of the tumor “immune” microenvironment (TIME). The expression of the Tn and STn antigens on tumors has been found to regulate the function of these immune cells and alter their normal antitumor cytotoxic role. This is possible through multiple cell intrinsic and extrinsic signaling pathways, elaborated in this review. Studying the interaction between Tn/STn antigens and the TIME of gastrointestinal cancers can help develop better and more robust therapies that can counteract immunosuppressive mechanisms to sensitize these tumors to anticancer therapies.
Chromatin mutations in pediatric high grade gliomas
Authors: Voon Hsiao P. J. , Wong Lee H.
Published: January 2023

Pediatric high grade gliomas (HGG) are lethal tumors which are currently untreatable. A number of recent studies have provided much needed insights into the mutations and mechanisms which drive oncogenesis in pediatric HGGs. It is now clear that mutations in chromatin proteins, particularly H3.3 and its associated chaperone complex (ATRX), are a hallmark feature of pediatric HGGs. We review the current literature on the normal roles of the ATRX/H3.3 complex and how these functions are disrupted by oncogenic mutations. We discuss the current clinical trials and pre-clinical models that target chromatin and DNA, and how these agents fit into the ATRX/H3.3 mutation model. As chromatin mutations are a relatively new discovery in pediatric HGGs, developing clear mechanistic insights are a key step to improving therapies for these tumors.
Comparison of clinical features and prognosis between ultrashort-segment and short-segment hirschsprung disease
Authors: Xie Chuanping , Yan Jiayu , Guo Jianlin , Liu Yakun , Chen Yajun
Published: January 2023

Objective

To compare the differences in clinical features, postoperative complications, and long-term bowel function outcomes of ultrashort-segment Hirschsprung disease (USHD) and short-segment Hirschsprung disease (SHD).

Methods

A retrospective study was conducted to compare patients with USHD or SHD who underwent transanal endorectal pull-through (TEPT) at Beijing Children's Hospital between January 2014 and June 2021. Clinical details were collected from medical records. A long-term bowel function questionnaire (age > 4 years old) was completed by the patients' parents.

Results

A total of 84 patients (USHD = 15, SHD = 69) were included. Age at diagnosis and radical surgery in the USHD group were significantly older than the SHD group (46 [38, 66] vs. 34 [6, 55] months, p = 0.002; 51 [39, 68] vs. 37 [10, 68] months, p = 0.001, respectively). Compared with the SHD group, patients with USHD are more likely to suffer anastomosis leakage and postoperative enterocolitis after TEPT ([3/15, 33.3%] vs. [1/69, 1.4%], p = 0.017; [5/15, 33.3%] vs. [6/69, 8.7%], p = 0.023). In addition, patients in the USHD group are inclined to suffer lower bowel function scores (12.0 [7.5, 18.3] vs. 17 [15, 19], p = 0.018).Patients in the USHD group were more likely to suffer poorer ability to hold back defecation (p = 0.023), soiling (p = 0.011), fecal accidents (p = 0.004), and social problems (p = 0.004).

Conclusion

Compared with patients with SHD, patients with USHD are diagnosed and performed TEPT at an older age. and they are inclined to suffer postoperative enterocolitis, anastomosis leakage, and poorer long-term bowel function following TEPT.
Severe pediatric Mycoplasma pneumonia as the cause of diffuse alveolar hemorrhage requiring veno-venous extracorporeal membrane oxygenation: A case report
Authors: Zhang Xinjuan , Yu Yanping
Published: January 2023

Background

Diffuse alveolar hemorrhage (DAH) is an acute life-threatening disease often associated with immunocompromised patients and systemic disorders, such as infections, vasculitis, and toxins. Mycoplasma pneumoniae is one of the most common causes of community-acquired pneumonia in children, which rarely causes respiratory failure and fulminant disease; However, a rapid progression may occur in some patients. Mycoplasma pneumonia-associated DAH is rare.

Case Presentation

We report a case of severe pediatric mycoplasma pneumonia in an immuno-competent child. This patient's condition progressed rapidly, with severe lung lesions associated with pleural effusion, coagulopathy, diffuse alveolar haemorrhage and severe respiratory distress requiring ventilator and intravenous extracorporeal membrane oxygenation (VV-ECMO) support. She was discharged upon successful treatment.

Conclusion

Diffuse alveolar hemorrhage associated with Mycoplasma pneumoniae in children is very rare, and clinicians should be aware of the potential rapid onset of the disease. Early detection and diagnosis are very important. The main treatment measures include anti-infection and supportive measures such as mechanical ventilation, but as in our case, success with both prone positioning for more than 10 h per day and VV-ECMO was life-saving.