Abundant Type Research Articles

HIV rebound in HIV controllers is associated with a specific fecal microbiome profile.

HIV infection is associated with gut dysbiosis, and microbiome variability may affect HIV control when antiretroviral therapy (ART) is stopped. The TLR7 agonist, vesatolimod, was previously associated with a modest delay in viral rebound following analytical treatment interruption in HIV controllers (HCs). Using a retrospective analysis of fecal samples from HCs treated with vesatolimod or placebo (NCT03060447), people with chronic HIV (CH; NCT02858401) or without HIV (PWOH), we examined fecal microbiome profile in HCs before/after treatment, and in CH and PWOH. Microbiome diversity and abundance were compared between groups to investigate the association between specific phyla/species, immune biomarkers, and viral outcomes during treatment interruption. Although there were no significant differences in gut microbiome diversity between people with and without HIV, HCs, and CH shared common features that distinguished them from PWOH. there was a trend toward greater microbiome diversity among HCs. Treatment with vesatolimod reduced dysbiosis in HCs. Firmicutes positively correlated with T-cell activation, while Bacteroidetes and Euryarchaeota inversely correlated with TLR7-mediated immune activation. Specific types of fecal microbiome abundance (e.g. Alistipes putredinis) positively correlated with HIV rebound. In conclusion, variability in the composition of the fecal microbiome is associated with markers of immune activation following vesatolimod treatment and ART interruption.

Proteomic changes in the human cerebrovasculature in Alzheimer's disease and related tauopathies linked to peripheral biomarkers in plasma and cerebrospinal fluid.

Cerebrovascular dysfunction is a pathological hallmark of Alzheimer's disease (AD). Nevertheless, detecting cerebrovascular changes within bulk tissues has limited our ability to characterize proteomic alterations from less abundant cell types. We conducted quantitative proteomics on bulk brain tissues and isolated cerebrovasculature from the same individuals, encompassing control (N=28), progressive supranuclear palsy (PSP) (N=18), and AD (N=21) cases. Protein co-expression network analysis identified unique cerebrovascular modules significantly correlated with amyloid plaques, cerebrovascular amyloid angiopathy (CAA), and/or tau pathology. The protein products within AD genetic risk loci were concentrated within cerebrovascular modules. The overlap between differentially abundant proteins in AD cerebrospinal fluid (CSF) and plasma with cerebrovascular network highlighted a significant increase of matrisome proteins, SMOC1 and SMOC2, in CSF, plasma, and brain. These findings enhance our understanding of cerebrovascular deficits in AD, shedding light on potential biomarkers associated with CAA and vascular dysfunction in neurodegenerative diseases.

Identification of microplastics in milkfish (Chanos chanos) in tradisional ponds in Pedaleman Village, Serang Regency

The entry of microplastic waste into pond waters come from household and fishing activities. This study aims to identify the presence of microplastics in milkfish in the Pedaleman Village pond by considering the type, color, and size of microplastics and to determine the polymers structure found in the digestive tract of milkfish. A total of 24 samples were collected directly from the pond in March to April 2023. The fish were measured for length (cm) and weight (g), and then dissected to remove the organs including digestive tract and muscle. The organs were then destroyed and microplastics were identified using microscope stereo. The fish organs were destroyed using 10% KOH after wet weight was measured. The sample were incubated for 24 hours until the organic matter was destroyed. Then, filtered using Whattman 42 paper and dried in an oven. The types of microplastics found in milkfish were fibers, films, and fragments. Fragment were the most abundant type of microplastics, followed by fiber and film. The fiber had a variety of colors, while the fragments are only found in black. The types of microplastic polymers found in milkfish intestines were polyethylene (PE), polytetrafluoroethylene (PTPE), Polymethyl methacrylate (PMMA), and nylon.

Abstract 2079: Single-cell And Spatially Resolved Transcriptome Analysis Reveals A Novel Lncrna Regulator Of Human Atherosclerosis

Cardiovascular diseases, such as atherosclerosis, are the major cause of death in Western societies. Still, molecular mechanisms of plaque destabilization remain unclear. Vascular Smooth Muscle Cells (VSMCs) are the most abundant cell type in atherosclerotic lesions. These cells keep their plasticity also with disease progression and are, therefore, an ideal target cell type for potential therapies. Long non-coding RNAs (lncRNAs) are one example of highly cell type- and disease-state-specific novel molecular modulators. We utilized combined total (bulk) RNA and single cell (sc) RNA sequencing of advanced human carotid artery lesions (patients who underwent carotid endarterectomy in our vascular surgery clinic) to discover novel regulators. Additionally, we performed hybridization-based RNA in situ sequencing (HybRISS, Xenium) to indicate where these genes are located within the plaques. We also performed scSeq in our inducible carotid artery plaque rupture mice ( ApoE-/- ). In vivo and in vitro modulation (KD; knock-down) of the newly identified lncRNA DLX6-AS1 ( D istal- L ess Homeobo x 6 A nti s ense 1 ) using Antisense LNA (Locked nucleic acid) GapmeRs is performed in this mouse model as well as in primary human VSMC culture. DLX6-AS1 shows a highly specific expression pattern in a distinct sub-cluster of VSMCs, as well as a striking location within human atherosclerotic lesions shown by spatial transcriptomics in advanced plaques. DLX6-AS1 is mainly expressed in the nucleus of cells, and KD of this lncRNA leads to changes in VSMC behavior in vitro and in vivo . The KD also has only little effect on the other genes of this locus, DLX6 and DLX5 ( D istal- L ess Homeobo x 6 and 5 ) We found Dlx6os1 ( D istal- l ess homeobo x 6, o pposite s trand 1 ) in our scRNA-seq dataset of the inducible carotid artery plaque rupture mice ( ApoE-/- ) where the KD leads to an increased plaque rupture rate. Taken together, our datasets, methods, and animal models demonstrate that utilizing bulk- and scRNA-seq data, together with spatially resolved sequencing methods, are powerful tools to identify and characterize novel lncRNA regulators that can facilitate fate decisions in VSMCs in atherosclerosis. DLX6-AS1 is one of these novel regulators and will be further analyzed in vivo and in vitro .

Abstract 2013: Smooth Muscle Cell-specific Deficiency Of Fibrillin-1 Induces Aortic Aneurysms But Does Not Disrupt Elastic Fiber Formation In Mice

Background and Aim: Fibrillin-1 has a complex biology that can influence elastic fiber formation and stability. Smooth muscle cells (SMCs), the most abundant cell type of the aortic wall, synthesize and secrete fibrillin-1. The purpose of this study was to determine the effects of fibrillin-1 (FBN1) synthesis in SMCs on elastic fiber formation and aortic pathologies. Methods and Results: We generated Fbn1 floxed mice that included the insertion of tdTomato as a reporter for gene deletion. Female Fbn1 floxed mice were bred with male Fbn1 floxed mice expressing Cre transgene driven by a Tagln promotor that led to the deletion of FBN1 in SMCs (SMC-FBN1-/-). Gene recombination was confirmed by the presence of tdTomato in the aorta of SMC-FBN1-/- mice. To determine the impact of SMC-specific FBN1 deletion on aortic integrity, SMC-FBN1 +/+ and -/- littermates were either terminated at 4 weeks of age with capture of in situ and ex vivo aortic images or aortas of live animals at 8 weeks of age were monitored using ultrasound. For mice terminated at 4 weeks of age, SMC-specific FBN1 deletion resulted in increased ascending aortic length (+/+ vs -/-: 2.9 vs 3.9 mm in males, p=0.004; +/+ vs -/-: 2.9 vs 3.5 mm in females, p=0.004) and width (+/+ vs -/-: 1.5 vs 1.9 mm in males, p=0.03; +/+ vs -/-: 1.4 vs 1.7 mm in females, p=0.02) of the ascending aorta and the aortic arch (+/+ vs -/-: 1.4 vs 1.9 mm in males, p<0.001; +/+ vs -/-: 1.4 vs 1.7 mm in females, p=0.01), whereas diameters of the descending thoracic aorta and suprarenal aorta were not different between SMC-FBN1 +/+ and SMC-FBN1-/- mice in either sex. Surprisingly, elastic fibers, as determined by Verhoff staining, were present in the media of each aortic region in SMC-FBN1-/- mice at 4 weeks of age, with comparable numbers of elastic lamellae as SMC-FBN1+/+ littermates in each sex. At 8 weeks of age, ultrasound detected profound luminal dilatations of the ascending aortic region and the suprarenal abdominal region in SMC-FBN1-/- mice, compared to their wild-type littermates. Conclusion: SMC-specific deficiency of FBN1 induced aortic aneurysms progressively, increasing with age, but did not overtly affect elastic fiber formation and the number of elastic lamina layers.

Marine litter along the shores of the Persian Gulf, Iran

Plastic wastes —including cigarette butts (CBs)— are dangerous for marine ecosystems not only because they contain hazardous chemicals but also because they can finally turn into micro- or even nano-particles that may be ingested by micro- and macro-fauna. Even large pieces of plastics can trap animals. In this research, the pollution status of macroplastics (abundance, size, type, and colour) and cigarette butts (CBs, number/m2) on the northern coasts of the Persian Gulf has been investigated. A total of 19 stations were explored in Bushehr province (Iran), which covers a length equivalent to 160 km of the Persian Gulf coastline. Among the collected plastic waste (2992 items), disposable mugs were the most frequent (18 %). Plastics with sizes 5–15 cm were the most abundant, and the most common type of plastic was PET (P-value <0.05). The origin of most macroplastics was domestic (2269 items). According to the Index of Clean Coasts (ICC), most surveyed beaches were extremely dirty. The average number and density of CBs in this study were 220 and 2.45 items/m2, respectively. Household litter was the most abundant type of waste in the studied beaches, and this problem can be better managed by training and improving the waste disposal culture. In general, it is suggested that an integrated and enhanced management for fishing, sewage and surface water disposal, and sandy recreational beaches be implemented in Bushehr to control plastic waste.

Single-Nuclei Characterization of Lacrimal Gland in Scopolamine-Induced Dry Eye Disease.

The lacrimal gland (LG) is the main organ responsible for tear secretion and an important pathogenic site for dry eye disease (DED). This study aimed to comprehensively characterize LG cellular heterogeneity under normal and DED conditions using single-nucleus RNA sequencing (snRNA-seq). Single LG nuclei isolated from mice with or without DED induced by scopolamine (SCOP)/desiccating stress (DS) were subjected to snRNA-seq using the 10x Genomics platform. These cells were clustered and annotated using the t-distributed stochastic neighbor embedding (t-SNE) method and unbiased computational informatic analysis. Cluster identification and functional analysis were performed based on marker gene expression and bioinformatic data mining. The snRNA-seq analysis of 30,351 nuclei identified eight major cell types, with acinar cells (∼72.6%) being the most abundant cell type in the LG. Subclustering analysis revealed that the LG mainly contained two acinar cell subtypes, two ductal cell subclusters, three myoepithelial cell (MECs) subtypes, and four immunocyte subclusters. In the SCOP-induced DED model, three major LG parenchymal cell types were significantly altered, characterized by a reduced proportion of acinar cells with a lowered secretion potential and an augmented proportion of ductal cells and MECs. LG immunocytes in DED scenarios showed an intensified inflammatory response and dysregulated intercellular communication with three major LG parenchymal cells. Overall, this study offers a systemic single-nucleus transcriptomic profile of LGs in both normal and DED conditions and an atlas of the complicated interactions of immunocytes with major LG parenchymal cells. The findings also facilitate understanding the pathogenesis of DED.

Association of Single Nucleotide Polymorphisms (SNPS) to Black Spot Resistance in Roses

Rose black spot caused by Diplocarpon rosae is the most severe and global disease of garden roses. Breeding of disease resistant varieties is one of the most important goals of modern garden rose breeding. Single nucleotide polymorphisms (SNPs) are the most abundant type of polymorphism found in eukaryotic genomes. SNP markers can be used in a wide variety of applications, including association studies, genetic diversity analysis, and marker-assisted selection in plant breeding programs. The aim of this project was to analyze black spot resistance in a rose association panel through leaf inoculation assays with single isolate pathotypes as well as a field mixture of D. rosae isolates and to establish a relationship between resistance and the available SNP markers. In this study, 96 diverse cultivars of roses were evaluated phenotypically for resistance against black spot through artificial inoculations. 63000 SNPs that were developed in previous studies were used to genetically analyze the cultivars and find associations with resistance against black spot disease using mixed linear model in TASSEL 3.0. Differences in the phenotypic reaction to field mixture of isolates and the Ab13 single conidial isolate of this pathogen were observed between genotypes. One hundred and forty-nine SNPs were found to be significantly associated with resistance against field mixtures of black spot. For the Ab13 single isolate, only one significant SNP was found. These SNPs were mapped on the rose chromosomes, and found on chromosome one, three and four. These associated SNP and Rdr1 markers can be used for marker-assisted selection in breeding for black spot resistance in rose.

Plastic litter assessment of the riverbanks of Pulot River and its tributary in Sofronio Española, Palawan Island, Philippines

Rivers are essential sources of plastic litter in the marine environment. Recently, the Philippines was reported as the biggest polluter of plastic litter from riverine sources. However, the riverine plastic litter's origin has been less established. In this study, we determined the density, composition, and accumulation of plastic litter on the riversides of Pulot River and its tributary in Palawan Island, Philippines. We also identified the possible sources of plastic litter. Results showed that the plastic litter density was highest at the river edge during the first sampling period. Litter densities for the predefined zones and sampling periods all showed no significant differences. The most dominant plastic litter types were food packaging and plastic bags, followed by toiletries. ‘Others’ consisted of multilayers, mixed, and plastics accounted for the most abundant polymer types. We identified the residents in the vicinity illegally dumping litter, for there were small illegal dumping sites along the river. These results suggest the urgent need for better waste policy implementation measures to protect the riparian environments and reduce the input of riverine plastic litter into the marine environment to ensure river resource sustainability.

Microplastic accumulation dynamics in Han river headwaters: Sediment interactions and environmental implication

The prevalence of microplastic (MP) contamination has become a significant environmental concern due to its pervasive nature and persistent effects. While sediments are considered major repositories for MPs, information on their spatial distribution within these matrices is insufficient. This research examined both the horizontal and vertical presence of MPs in the sediments surrounding Lake Paldang in South Korea, alongside a comprehensive evaluation of the physicochemical characteristics of the samples obtained. The total content of MPs varied from 2.15 to 122.2 particles g−1. The average contents of MPs on surface sediments were 40.47, 34.14, 5.01, and 8.19 particles g−1 in north mainstream (NM), south mainstream (SM), tributary (TB), and Tributary catchment (TC) based on Sonae Island, Gyeongan stream, respectively. The most abundant MP types were polyethylene (PE), polytetrafluoroethylene (PTFE), and polypropylene (PP), accounting for more than 70% of the total MPs. The most abundant sizes of MPs were within 45–100 µm. At all sediment depths, polymers were distributed in the order PE, PP, and polyester in NM, SM, and TC, respectively, whereas PTFE mainly occurred in the surface layer. MPs distribution also exhibited seasonal variation as larger inflows and flow rates varied with season.

Oviposition site selection and subsequent offspring performance of Aedes aegypti in short- and long-term detritus accumulation conditions

The “oviposition preference-offspring performance” hypothesis proposes that females lay their eggs in habitats that maximize the fitness of their offspring. The aim of this study was to assess the oviposition site selection by Aedes aegypti females and the success of their larvae in habitats with different detritus accumulation times, under conditions representative of the natural spatial variability of detritus quality and quantity in the Metropolitan Area of Buenos Aires, Argentina. Two experiments were performed, one assessing oviposition site selection and the other analyzing developmental success. In both experiments, two levels of detritus accumulation time were compared, one with short-time detritus accumulation (2 weeks), and the other with long-time detritus accumulation (8 weeks). Naturally fallen detritus was used in both experiments, collected in ten sites across the Metropolitan Area of Buenos Aires. In the oviposition experiment, two contiguous ovitraps corresponding to each accumulation time were placed at each of the ten sites and the number of eggs received for each accumulation time was compared. In the development experiment, always 19 larvae were raised in containers of both accumulation times and overall performance was compared using an integrated index that considers survival, development time and female size. A large variability in the amount of detritus collected at the different sites was observed. The number of eggs was significantly higher in the long-time than in the short-time detritus accumulation containers, and approximately proportional to the amount of detritus in each ovitrap. The performance was not affected by the detritus accumulation time, but a better performance was detected in containers that received a higher amount of organic detritus, regardless of the accumulation time. Leaves were on average the most abundant type of detritus, with an average of 53 % of the total detritus collected. The amount of leaves added 2 weeks before hatching showed a positive effect on larval performance. Our results do not support the “oviposition preference-offspring performance” hypothesis, since Ae. aegypti females laid eggs in containers where larvae did not show a better performance. Moreover, at larval densities related to the number of eggs actually laid in each of the accumulation times, it is expected that the performance would be even worse in the most selected containers, due to the density-dependent effects of crowding. Since the results obtained reflect the natural heterogeneity of the environmental conditions in the region studied, they might be a fairly good indicator of what occurs in natural larval habitats.

Lineage tracing reveals a novel PDGFRβ+ satellite cell subset that contributes to myo-regeneration of chronically injured rotator cuff muscle

Massive rotator cuff (RC) tendon tears are associated with progressive fibro-adipogenesis and muscle atrophy that altogether cause shoulder muscle wasting. Platelet derived growth factor β (PDGFRβ) lineage cells, that co-express PDGFRα have previously been shown to directly contribute to scar formation and fat accumulation in a mouse model of irreversible tendon and nerve transection (TTDN). Conversely, PDGFRβ+ lineage cells have also been shown to be myogenic in cultures and in other models of skeletal muscle injury. We therefore hypothesized that PDGFRβ demarcates two distinct RC residing subpopulations, fibro-adipogenic and myogenic, and aimed to elucidate the identity of the PDGFRβ myogenic precursors and evaluate their contribution, if any, to RC myo-regeneration. Lineage tracing revealed increasing contribution of PDGFRβ+ myo-progenitors to the formation of GFP+ myofibers, which were the most abundant myofiber type in regenerated muscle at 2 weeks post-TTDN. Muscle regeneration preceded muscle atrophy and both advanced from the lateral site of tendon transection to the farthest medial region. GFP+/PDGFRβ+Sca-1−lin−CXCR4+Integrin-β1+ marked a novel subset of satellite cells with confirmed myogenic properties. Further studies are warranted to identify the existence of PDGFRβ+ satellite cells in human and other mouse muscles and to define their myo-regenerative potential following acute and chronic muscle injury.

CircCOL1A1 promotes proliferation, migration, and invasion of colorectal cancer (CRC) cells and glutamine metabolism through GLS1 up-regulation by sponging miR-214-3p

BackgroundCircular ribose nucleic acids (circRNAs), an abundant type of noncoding RNAs, are widely expressed in eukaryotic cells and exert a significant impact on the initiation and progression of various disorders, including different types of cancer. However, the specific role of various circRNAs in colorectal cancer (CRC) pathology is still not fully understood.MethodsThe initial step involved the use of quantitative reverse transcription polymerase chain reaction (RT-qPCR) to assess the expression levels of circRNAs and messenger RNA (mRNA) in CRC cell lines and tissues. Subsequently, functional analyses of circCOL1A1 knockdown were conducted in vitro and in vivo through cell counting kit (CCK)-8, colony formation and transwell assays, as well as xenograft mouse model of tumor formation. Molecular expression and interactions were investigated using luciferase reporter assays, Western blot analysis, RNA immunoprecipitation (RIP), and immunohistochemical staining.ResultsThe RT-qPCR results revealed elevated levels of circCOL1A1 expressions in CRC tissues and cell lines as compared to the normal counterparts. In addition, circCOL1A1 expression level was found to be correlated with TNM stage, lymph node metastases, distant metastases, and invasion. Knockdown of circCOL1A1 resulted in impaired invasion, migration, and proliferation of CRC cells, and suppressed tumor generation in the animal model. We further demonstrated that circCOL1A1 could act as a sponge for miR-214-3p, suppressing miR-214-3p activity and leading to the upregulation of GLS1 protein to promote glutamine metabolism.ConclusionThese findings suggest that circCOL1A1 functions as an oncogenic molecule to promote CRC progression via miR-214-3p/GLS1 axis, hinting on the potential of circCOL1A1 as a therapeutic target for CRC.

Heterocellular Adhesion in Cancer Invasion and Metastasis: Interactions between Cancer Cells and Cancer-Associated Fibroblasts.

Cancer invasion is a requisite for the most malignant progression of cancer, that is, metastasis. The mechanisms of cancer invasion were originally studied using in vitro cell culture systems, in which cancer cells were cultured using artificial extracellular matrices (ECMs). However, conventional culture systems do not precisely recapitulate in vivo cancer invasion because the phenotypes of cancer cells in tumor tissues are strongly affected by the tumor microenvironment (TME). Cancer-associated fibroblasts (CAFs) are the most abundant cell type in the TME and accelerate cancer progression through invasion, metastasis, therapy resistance, and immune suppression. Thus, the reciprocal interactions between CAFs and cancer cells have been extensively studied, leading to the identification of factors that mediate cellular interactions, such as growth factors, cytokines, and extracellular vesicles. In addition, the importance of direct heterocellular adhesion between cancer cells and CAFs in cancer progression has recently been elucidated. In particular, CAFs are directly associated with cancer cells, allowing them to invade the ECM and metastasize to distant organs. In this review, we summarize the recent progress in understanding the molecular and cellular mechanisms of the direct heterocellular interaction in CAF-led cancer invasion and metastasis, with an emphasis on gastric cancer.

A review on the presence of microplastics in environmental matrices within Southeast Asia: elucidating risk information through an analysis of microplastic characteristics such as size, shape, and type

Microplastics’ ecotoxicological potential in almost all ecosystems makes them a global environmental issue. This review evaluates Southeast Asian microplastic contamination data from 2013 to 2023. This evaluation examined 285 research publications from Scopus, Web of Science, and ScienceDirect, mostly on sediment and water matrices. Based on their size, shape, polymer type, and potential risks from polymer hazards in Southeast Asian countries, this analysis assesses microplastic pollution in biota, sediment, water, and other environmental matrices. The majority of microplastics in this region are small (46%) and large (32%). Within the biota matrix, small microplastics (SMP) and large microplastics (LMP) dominated. Fibers predominated in all matrices, particularly the biota matrix. Polyethylene emerged as the most abundant polymer type (22%), found in all four matrices. Despite being less abundant, polyurethane and polyamide have high hazard scores, raising ecological concerns due to their detrimental effects on environmental matrices. According to the analyzed data, Southeast Asian countries face significant risks due to high levels of microplastic contamination in water, sediments, biota, and other matrices. However, there are noticeable discrepancies in Southeast Asian data, indicating progress in microplastic research, with most data coming from Indonesia, Thailand, Malaysia, Vietnam, and the Philippines and little information in the literature regarding microplastic contamination from East Timor, Laos, Brunei, Myanmar, and Cambodia.

A comprehensive review of m6A research in cervical cancer.

Cervical cancer (CC) remains one of the most common malignancies among women worldwide, posing a serious threat to women's health. N6-methyladenosine (m6A) modification, as the most abundant type of RNA methylation modification, and has been found to play a crucial role in various cancers. Current research suggests a close association between RNA m6A modification and the occurrence and progression of CC, encompassing disruptions in m6A levels and its regulatory machinery. This review summarizes the current status of m6A modification research in CC, explores the mechanisms underlying m6A levels and regulators (methyltransferases, demethylases, reader proteins) in CC and examines the application of small-molecule inhibitors of m6A regulators in disease treatment. The findings provide new insights into the future treatment of CC.

Network-level encoding of local neurotransmitters in cortical astrocytes

Astrocytes, the most abundant non-neuronal cell type in the mammalian brain, are crucial circuit components that respond to and modulate neuronal activity through calcium (Ca2+) signalling1–7. Astrocyte Ca2+ activity is highly heterogeneous and occurs across multiple spatiotemporal scales—from fast, subcellular activity3,4 to slow, synchronized activity across connected astrocyte networks8–10—to influence many processes5,7,11. However, the inputs that drive astrocyte network dynamics remain unclear. Here we used ex vivo and in vivo two-photon astrocyte imaging while mimicking neuronal neurotransmitter inputs at multiple spatiotemporal scales. We find that brief, subcellular inputs of GABA and glutamate lead to widespread, long-lasting astrocyte Ca2+ responses beyond an individual stimulated cell. Further, we find that a key subset of Ca2+ activity—propagative activity—differentiates astrocyte network responses to these two main neurotransmitters, and may influence responses to future inputs. Together, our results demonstrate that local, transient neurotransmitter inputs are encoded by broad cortical astrocyte networks over a minutes-long time course, contributing to accumulating evidence that substantial astrocyte–neuron communication occurs across slow, network-level spatiotemporal scales12–14. These findings will enable future studies to investigate the link between specific astrocyte Ca2+ activity and specific functional outputs, which could build a consistent framework for astrocytic modulation of neuronal activity.

Look4LTRs: a Long terminal repeat retrotransposon detection tool capable of cross species studies and discovering recently nested repeats

Plant genomes include large numbers of transposable elements. One particular type of these elements is flanked by two Long Terminal Repeats (LTRs) and can translocate using RNA. Such elements are known as LTR-retrotransposons; they are the most abundant type of transposons in plant genomes. They have many important functions involving gene regulation and the rise of new genes and pseudo genes in response to severe stress. Additionally, LTR-retrotransposons have several applications in biotechnology. Due to the abundance and the importance of LTR-retrotransposons, multiple computational tools have been developed for their detection. However, none of these tools take advantages of the availability of related genomes; they process one chromosome at a time. Further, recently nested LTR-retrotransposons (multiple elements of the same family are inserted into each other) cannot be annotated accurately — or cannot be annotated at all — by the currently available tools. Motivated to overcome these two limitations, we built Look4LTRs, which can annotate LTR-retrotransposons in multiple related genomes simultaneously and discover recently nested elements. The methodology of Look4LTRs depends on techniques imported from the signal-processing field, graph algorithms, and machine learning with a minimal use of alignment algorithms. Four plant genomes were used in developing Look4LTRs and eight plant genomes for evaluating it in contrast to three related tools. Look4LTRs is the fastest while maintaining better or comparable F1 scores (the harmonic average of recall and precision) to those obtained by the other tools. Our results demonstrate the added benefit of annotating LTR-retrotransposons in multiple related genomes simultaneously and the ability to discover recently nested elements. Expert human manual examination of six elements — not included in the ground truth — revealed that three elements belong to known families and two elements are likely from new families. With respect to examining recently nested LTR-retrotransposons, three out of five were confirmed to be valid elements. Look4LTRs — with its speed, accuracy, and novel features — represents a true advancement in the annotation of LTR-retrotransposons, opening the door to many studies focused on understanding their functions in plants.

Impaired astrocytic synaptic function by peripheral cholesterol metabolite 27-hydroxycholesterol.

Astrocytes represent the most abundant cell type in the brain, where they play critical roles in synaptic transmission, cognition, and behavior. Recent discoveries show astrocytes are involved in synaptic dysfunction during Alzheimer's disease (AD). AD patients have imbalanced cholesterol metabolism, demonstrated by high levels of side-chain oxidized cholesterol known as 27-hydroxycholesterol (27-OH). Evidence from our laboratory has shown that elevated 27-OH can abolish synaptic connectivity during neuromaturation, but its effect on astrocyte function is currently unclear. Our results suggest that elevated 27-OH decreases the astrocyte function in vivo in Cyp27Tg, a mouse model of brain oxysterol imbalance. Here, we report a downregulation of glutamate transporters in the hippocampus of CYP27Tg mice together with increased GFAP. GLT-1 downregulation was also observed when WT mice were fed with high-cholesterol diets. To study the relationship between astrocytes and neurons, we have developed a 3D co-culture system that allows all the cell types from mice embryos to differentiate in vitro. We report that our 3D co-cultures reproduce the effects of 27-OH observed in 2D neurons and in vivo. Moreover, we found novel degenerative effects in astrocytes that do not appear in 2D cultures, together with the downregulation of glutamate transporters GLT-1 and GLAST. We propose that this transporter dysregulation leads to neuronal hyperexcitability and synaptic dysfunction based on the effects of 27-OH on astrocytes. Taken together, these results report a new mechanism linking oxysterol imbalance in the brain and synaptic dysfunction through effects on astrocyte function.

ABUNDANCE OF MARINE DEBRIS ON PADANG AND PARIAMAN BEACHES WEST SUMATRA PROVINCE

Padang and Pariaman Beaches are regional strategic locations for tourism and have been growing rapidly. However, waste has become a significant concern because of its anthropogenic impact. This study aims to identify and analyze the types of waste abundance on both beaches of these tourist destinations. This research was conducted in August 2022 using a survey method. This study found eight types of waste in the two locations. They comprise plastic, metal, glass, wood, paper, rubber, and cloth fragments. The total fragment on Padang Beach reached 3,392 items/m2, higher during the weekend than before the weekend (1,212 and 1,072 items/m2). Meanwhile, the total fragment on Pariaman Beach reached 2,484 items/m2 and was higher during the weekends than after the weekends (0.956 and 0.74 items/m2). Moreover, there was no significant difference between the two locations (p&gt;0.05). It might relate to the characteristics of the same water quality parameters: the current velocity ranges from 0.3-0.4 m/s (medium current), so it does not have a different effect.