bluuebunny/crossref_metadata_2025 huggingface dataset:
Controlling critical mistag-associated false discoveries in metagenetic data
Authors: Richardson Rodney T.
Published: January 2022

Metagenetic methods are commonplace within ecological and environmental research. One concern with these methods is the phenomenon of critical mistagging, where sequences from one sample are erroneously inferred to have originated from another sample due to errors in the attachment, PCR replication or sequencing of sample-specific dual-index tags. For studies using PCR-based library preparation on large sample sizes, the most cost-effective approach to limiting mistag-associated false detections involves using an unsaturated Latin square dual-indexing design. This allows researchers to estimate mistagging rates during sequencing but the statistical procedures for filtering out detections using this mistag rate have received little attention.

We propose a straightforward method to limit mistag-associated false discoveries during metabarcoding applications. We analyzed two Illumina metabarcoding datasets produced using unsaturated Latin square designs to explore the distribution of mistagged sequences across dual-index combinations on a per taxon basis. We tested these data for conformity to the assumptions that 1) mistagging follows a binomial distribution [i.e.,X~B(n, p)] wherep, the probability of a sequence being mistagged, varies minimally across taxa and 2) mistags are distributed uniformly across dual-index combinations. We provide R functions that estimate the 95thpercentile of expected mistags per dual-index combination for each taxon under these assumptions.

We show that mistagging rates were consistent across taxa within the datasets analyzed and that modelling mistagging as a binomial process with uniform distribution across dual-index combinations enabled robust control of mistag-associated false discoveries.

We propose that this method of taxon-specific filtering of detections based on the maximum mistags expected per dual-index combination should be broadly accepted during metagenetic analysis, provided that experimental and control sequence abundances per taxon are strongly correlated. When this assumption is violated, data may be better fit by assuming that the distribution of mistags across combinations follows Poisson characteristics [i.e.,X~ Pois(λ)], withλempirically estimated from the abundance distribution of mistags among control samples. We provide a second R function for this case, though we have yet to observe such a dataset. Both functions and demonstrations associated with this work are freely available athttps://github.com/RTRichar/ModellingCriticalMistags.
Meta-analysis of the genetic loci of pigment pattern evolution in vertebrates
Authors: Elkin Joel , Martin Arnaud , Courtier-Orgogozo Virginie , Santos M. Emília
Published: January 2022

Vertebrate pigmentation patterns are amongst the best characterised model systems for studying the genetic basis of adaptive evolution. The wealth of available data on the genetic basis for pigmentation evolution allows for meta-analysis of trends and quantitative testing of evolutionary hypotheses. We employed Gephebase, a database of genetic variants associated with natural and domesticated trait variation, to examine trends in howcis-regulatory and coding mutations contribute to vertebrate pigmentation phenotypes, as well as factors that favour one mutation type over the other. We found that studies with lower ascertainment bias identified higher proportions ofcis-regulatory mutations, and thatcis-regulatory mutations were more common amongst animals harboring a higher number of pigment cell classes. We classified pigmentation traits firstly according to their physiological basis and secondly according to whether they affect colour or pattern, and identified that carotenoid-based pigmentation and variation in pattern boundaries are preferentially associated withcis-regulatory change. We also classified genes according to their developmental, cellular, and molecular functions. We found that genes implicated in upstream developmental processes had greatercis-regulatory proportions than downstream cellular function genes, and that ligands were associated with highercis-regulatory proportions than their respective receptors. Based on these trends, we discuss future directions for research in vertebrate pigmentation evolution.
Investigating neurotrophin genetics and hippocampal volume
Authors: de Frutos Lucas Jaisalmer , Vacher Michael , Porter Tenielle , Brown Belinda , Laws Simon
Published: January 2022

As individuals get older, the structural integrity of brain regions becomes progressively diminished. Neurotrophic function might aid in preventing such losses through increased synaptogenesis and neurogenesis, particularly in the hippocampus, a brain structure relevant for cognitive function. However, the carriage of certain genetic alleles for genes involved in neurotrophic function might restrain the effectiveness of neurotrophin signalling, hindering neuroprotection. Yet, research on the contribution of single nucleotide polymorphisms (SNPs) within genes coding for neurotrophins and their receptors to hippocampal volumes is scarce, with the exception of rs6265 within the brain-derived neurotrophic factor gene. Therefore, the aim of this study was to identify SNPs within genes involved neurotrophic function that are associated with hippocampal volume in a sample of 23,776 cognitively normal older adults from the UK Biobank. We found that, in individuals older than 50, homozygote carriage of the major alleles rs4839435-A within nerve growth factor gene and rs56405676-T within the neurotrophic receptor tyrosine kinase 2 gene, were associated with increase hippocampal volumes, compared to carriage of 1 or 2 copies of the minor alleles. However, only rs56405676-T was significantly associated with greater hippocampal volumes in individuals older than 60. Hence this study might serve to identify populations at higher risk of hippocampal attrition and cognitive decline.
Phase tracking algorithms detect both real and imaginary components of outer hair cell nonlinear membrane capacitance that exhibits dielectric loss
Authors: Santos-Sacchi Joseph
Published: January 2022

Outer hair cell (OHC) nonlinear membrane capacitance (NLC) represents voltage-dependent sensor charge movements within prestin (SLC26a5) that drive OHC electromotility. Dielectric loss, a shift in charge movement phase from purely “capacitive” to “resistive”, is likely indicative of prestin’s interaction with the viscous lipid bilayer and has been suggested to correspond to prestin power output. The frequency response of NLC in OHC membrane patches has been measured with phase tracking and complex capacitance methodologies. While the latter approach can directly determine the presence of dielectric loss by assessing charge movement both in and out of phase with driving voltage, the former has been suggested to fail in this regard. Here we show that standard phase tracking in the presence of dielectric loss does indeed register this loss. Such estimates of NLC correspond to the absolute magnitude of complex NLC, indicating that total charge movement regardless of phase is assessed, thereby validating past and present measures of NLC frequency response that limits its effectiveness at high frequencies. This observation has important implications for understanding prestin’s role in cochlear amplification.
Bacterial composition and inferring function profiles in the biofloc system rearing Litopenaeus vannamei postlarvae at a low salinity
Authors: Huang Hai-Hong , Li Chao-Yun , Lei Yan-Ju , Kuang Wei-Qi , Zou Wan-Sheng , Yang Pin-Hong
Published: January 2022

This study aimed to investigate the bacterial composition and inferring function profiles in the biofloc system rearing Litopenaeus vannamei postlarvae (PL) at a low salinity condition. PL (~ stage 15) were stocked in four parallel tanks filled in water with a salinity of 5.0‰ at a density of 4000 individuals per m3 for a 28-days culture experiment, during which glucose was added as carbon source with a C:N of 20:1. At the end of experiment, water was sampled from each tank and pooled to extract microbial DNA for high-throughput sequencing of V3-V4 region of 16S rRNA gene. Results showed that the bacterial community at 28 d was dominated by phyla of Proteobacteria (45.8%), Bacteroidetes (21.1%), Planctomycetes (13.5%), Chlamydiae (10.3%) and Firmicutes (6.8%). A proportion of 81% inferring KEGG functions of this bacterial community associated with metabolism. Among functions relating to nitrogen metabolism, 48.5% were involved in the conversion of ammonia to glutamate, but the proportion of those involved in transformation among ammonia, nitrite and nitrate was 18.0% in total, inferring higher protein-synthesis but lower inorganic nitrogen-transformation capacities of the bacterial community. At the same time (28 d), high levels of total nitrogen (231.3±6.0 mg L-1) and biofloc (127.0±63.0 mL L-1), but low concentrations of ammonia (0.04±0.01 mg L-1), nitrite (0.2±0.1 mg L-1) and nitrate (12.9±2.5 mg L-1) were observed. The results supply a novel insight for understanding the function of bacterial community in the biofloc system nursing L. vannamei PL at a low salinity.
Cooperative regulation of C1-domain membrane recruitment polarizes atypical Protein Kinase C
Authors: Jones Kimberly A. , Drummond Michael L. , Penkert Rhiannon R. , Prehoda Kenneth E.
Published: January 2022

Recruitment of the Par complex protein atypical Protein Kinase C (aPKC) to a specific membrane domain is a key step in the polarization of animal cells. While numerous proteins and phospholipids interact with aPKC, how these interactions cooperate to control its membrane recruitment has been unknown. Here we identify aPKC’s C1 domain as a phospholipid interaction module that targets aPKC to the membrane ofDrosophilaneural stem cells (NSCs). The isolated C1 binds the NSC membrane in an unpolarized manner during interphase and mitosis and is uniquely sufficient among aPKC domains for targeting. Other domains, including the catalytic module and those that bind the upstream regulators Par-6 and Bazooka, restrict C1’s membrane targeting activity – spatially and temporally – to the apical NSC membrane during mitosis. Our results suggest that aPKC polarity results from cooperative activation of autoinhibited C1-mediated membrane binding activity.
Development, Structure, and Mechanism of Synthetic Antibodies that Target Claudin and Clostridium perfringens Enterotoxin Complexes
Authors: Orlando Benjamin J. , Dominik Pawel K. , Roy Sourav , Ogbu Chinemerem , Erramilli Satchal K. , Kossiakoff Anthony A. , Vecchio Alex J.
Published: January 2022

Strains of the Gram-positive bacterium Clostridium perfringens produce a two-domain enterotoxin (CpE) that afflict millions of humans and domesticated animals annually by causing prevalent gastrointestinal illnesses. CpE’s C-terminal domain (cCpE) binds cell surface receptors then its N-terminal domain restructures to form a membrane-penetrating β-barrel pore, which is toxic to epithelial cells of the gut. The claudin family of membrane proteins are the receptors for CpE, and also control the architecture and function of cell/cell contacts called tight junctions that create barriers to intercellular transport of solutes. CpE binding disables claudin and tight junction assembly and induces cytotoxicity via β-pore formation, disrupting gut homeostasis. Here, we aimed to develop probes of claudin/CpE assembly using a phage display library encoding synthetic antigen-binding fragments (sFabs) and discovered two that bound complexes between human claudin-4 and cCpE. We established each sFab’s unique modes of molecular recognition, their binding affinities and kinetics, and determined structures for each sFab bound to ~35 kDa claudin-4/cCpE in three-protein comprised complexes using cryogenic electron microscopy (cryoEM). The structures reveal a recognition epitope common to both sFabs but also that each sFab distinctly conforms to bind their antigen, which explain their unique binding equilibria. Mutagenesis of antigen/sFab interfaces observed therein result in further binding changes. Together, these findings validate the structures and uncover the mechanism of targeting claudin-4/cCpE complexes by these sFabs. Based on these structural insights we generate a model for CpE’s cytotoxic claudin-bound β-pore that predicted that these two sFabs would not prevent CpE cytotoxicity, which we verify in vivo with a cell-based assay. This work demonstrates the development and targeting mechanisms of sFabs against claudin/cCpE that enable rapid structural elucidation of these small membrane protein complexes using a cryoEM workflow. It further provides a structure-based framework and therapeutic strategies for utilizing these sFabs as molecular templates to target claudin/CpE assemblies, obstruct CpE cytotoxicity, and treat CpE-linked gastrointestinal diseases that cause substantial economic and quality of life losses throughout the world.
Role of vegetation characteristics on the distribution of three hornbill species in and around Pakke Tiger Reserve, Arunachal Pradesh, India
Authors: Dasgupta Soumya , Bhattacharya Tapajit , Kaul Rahul
Published: January 2022

The relationship between various vegetation characteristics and the relative abundance of three hornbill species [Great Pied Hornbill (Buceros bicornis), Wreathed Hornbill (Rhyticeros undulatus) and Oriental Pied Hornbill (Anthracoceros albirostris)] was studied in and around Pakke Tiger Reserve, Arunachal Pradesh. We walked transects (n=11; 22 walks) in three study sites to detect hornbills. Vegetation sampling was done using circular plots (n=33; 10 m radius) at every 400m interval along each transect. Encounter rate (1.5± 0.188/km) of Great Pied Hornbill (Buceros bicornis) was highest in the protected and undisturbed forest area where food and roosting tree density were also high (114/ha). Oriental Pied Hornbill was common in both the sites within Pakke Tiger reserve near riverine forests (0.75±0.25/km) and also in the dense undisturbed forest (0.875±0.226/km). Multivariate analysis revealed that tree density, presence of fruiting trees (utilized by hornbills), canopy cover, and tree diversity in a particular area are the major factors responsible for the assemblage of more than one species of hornbills. The study shows that protection of the forest patches to keep the diversity and density of the tree species intact is crucial for the survival and distribution of the hornbills in the landscape.
Genetically-linked simultaneous overexpression of multiple herbicide-metabolizing genes for broad-spectrum resistance in an agricultural weed Echinochloa phyllopogon
Authors: Suda Hiroe , Kubo Tomomi , Yoshimoto Yusuke , Tanaka Keisuke , Tanaka Satoru , Uchino Akira , Azuma Satoshi , Hattori Makoto , Yamaguchi Takuya , Miyashita Masahiro , Tominaga Tohru , Iwakami Satoshi
Published: January 2022

Previous research unveiled that the overexpression of catalytically promiscuous CYP81A cytochrome P450s underlies the multiple-herbicide resistance (MHR) in a Californian population of Echinochloa phyllopogon. However, it does not fully accommodate the resistance to diverse herbicides in MHR E. phyllopogon although the genetic inheritance of MHR was suggested as under a single gene control.

We investigated the high-level resistance to diclofop-methyl in MHR E. phyllopogon. Detailed diclofop-methyl metabolism was analyzed, followed by gene expression study and functional characterization of P450 genes. The generality of the MHR mechanism was investigated using another MHR line.

The MHR line rapidly produced two distinct hydroxylated-diclofop-acid, only one of which was the major metabolite produced by CYP81A12/21. Gene expression study identified the genetically linked overexpression of a novel gene CYP709C69 with CYP81A12/21 in the MHR line. The gene conferred diclofop-methyl resistance in plants and produced another hydroxylated-diclofop-acid in yeast. The activity was observed in some CYP709C in plants. Unlike the broad substrate-specificity in CYP81As, CYP709C69 showed narrow substrate-specificity. The overexpression of the CYP81A and CYP709C69 was also observed in another MHR line.

The present findings establish a novel concept that genetically-linked simultaneous overexpression of herbicide-metabolizing genes enhances and broadens the profile of metabolic resistance in weeds.
An ultra-sensitive and easy-to-use multiplexed single-cell proteomic analysis
Authors: Gu Lei , Li Ziyi , Wang QinQin , Zhang HuiPing , Sun YiDi , Li Chen , Wang Hui
Published: January 2022

Proteins analysis from an average cell population often overlooks the cellular heterogeneity of expressed effector molecules, and knowledge about the regulations of key biological processes may remain obscure. Therefore, the necessity of single-cell proteomics (SCP) technologies arises. Without microfluidic chip, expensive ultrasonic equipment, or reformed liquid chromatogram (LC) system, we established an Ultra-sensitive and Easy-to-use multiplexed Single-Cell Proteomic workflow (UE-SCP). Specifically, the flexible sorting system ensured outstanding cell activity, high accuracy, remarkable efficiency, and robustness during single-cell isolation. Multiplex isobaric labeling realized the high-throughput analysis in trapped ion mobility spectrometry coupled with quadrupole time-of-flight mass spectrometry (timsTOF MS). Using this pipeline, we achieved single-cell protein quantities to a depth of over 2,000 protein groups in two human cell lines, Hela and HEK-293T. A small batch experiment can identify and quantify more than 3200 protein groups in 32 single cells, while a large batch experiment can identify and quantify about 4000 protein groups in 96 single cells. All the 128 single cells from different cell lines could been unsupervised clustered based on their proteomes. After the integration of data quality control, data cleaning, and data analysis, we are confident that our UE-SCP platform will be easy-to-marketing popularization and will promote biological applications of single-cell proteomics.
Capsaicin potently blocks Salmonella typhimurium invasion of Vero cells
Authors: Ayariga Joseph A. , Abugri Daniel A. , Amrutha Balagopal , Villafane Robert
Published: January 2022

As at 2021, the center for disease control (CDC) reported that Salmonella causes 1.2 million illness in the United States each year, with a mortality rate approaching 500 deaths per annum. Infants, the elderly, and persons with compromised immunity are the population with higher risk of mortality from this infection. At present there is no commercially available, safe and efficacious vaccine for the control and management of Salmonella typhimurium (S. typhimurium). More so, S. typhimurium has been shown to develop resistance against most antibiotics used for treatment of the infection. Capsaicin, a bioactive compound from Capsicum chinense (C. chinenses) is undoubtedly one of the most widely used spice in the world. This heat producing compound is not only been used as food additive but have been demonstrated to possess unique properties that have pharmacological, physiological, and antimicrobial applications. In this work, the antimicrobial property of pure capsaicin or capsaicin extract against S. typhimurium is tested to determine the compounds effectiveness in S. typhimurium inhibition. Capsaicin extract showed potent inhibition of S. typhimurium growth at concentrations as low as 100 ng/ml, whereas pure capsaicin comparatively showed poorer inhibition of the bacteria. Furthermore, both capsaicin extract and pure capsaicin potently blocked S. typhimurium invasion of an animal cell line in vitro. Taken together, this work revealed that capsaicin might work synergistically with dihydrocapsaicin or the other capsaicinoids to inhibit S. typhimurium growth, whereas individually, capsaicin or dihydrocapsaicin could potently block the bacteria entry and invasion of Vero cells.
Temporal variation of patch connectivity determines biodiversity recovery from recurrent disturbances
Authors: Jacquet Claire , Munoz François , Bonada Núria , Datry Thibault , Heino Jani , Jabot Franck
Published: January 2022

Understanding the capacity of ecological systems to withstand and recover from disturbances is a major challenge for ecological research in the context of environmental change. Disturbances have multi-scale effects: they can cause species extinctions locally and alter connectivity between habitat patches at the metacommunity level. Yet, our understanding of how disturbances influence landscape connectivity remains limited. To fill this gap, we develop a novel connectivity index that integrates the temporal variation of patch connectivity induced by disturbances, which can be applied to any spatially-structured habitat. We then combine this index with a metacommunity model to specifically investigate biodiversity recovery from drying events in river network metacommunities. We demonstrate that patch connectivity explains variations of species richness between groups of organisms with contrasting dispersal modes and captures the effect of drying intensity (i.e., fraction of patches that dry-up) and drying location on community recovery. As a general rule, loss of patch connectivity decreases community recovery, regardless of patch location in the river network, dispersal mode, or drying intensity. Local communities of flying organisms maintained higher patch connectivity in drying river networks compared to organisms with strictly aquatic dispersal, which explained the higher recovery capacity of this group from drying events. The general relationship between patch connectivity and community recovery we found can be applied to any spatial network subject to temporal variation of connectivity, thus providing a powerful tool for biodiversity management in dynamic landscapes.
Deriving observation distances for camera trap distance sampling
Authors: Zuleger Annika M. , Holland Ruben , Kühl Hjalmar S.
Published: January 2022

Camera trap distance sampling (CTDS)o is a recently developed survey method to estimate animal abundance from camera trap data for unmarked populations. It requires the estimation of camera‐animal observation distances, which previously was done by comparing animal positions to reference labels at predefined intervals. Here, we test a photogrammetry approach to derive camera‐animal observation distances. We applied both, the reference label and photogrammetry approaches to five ungulate species varying widely in body size (Giraffa camelopardalis,Equus grevyi,Oryx dammah,Kobus megacerosandEudorcas thomsonii) and one ground‐dwelling bird species (Numida meleagris) inhabiting a large enclosure and estimated their density with CTDS. Both procedures provided highly correlated observation distances (ρ = 0.99,p < 0.001). A paired t test revealed a minor but significantly higher mean of the photogrammetry approach (MD = 0.28 m,p < 0.001). This, however, seems negligible as for analyses, distances were grouped in intervals of 2 to 5 metres. In general, estimated animal abundance was close to the true number of individuals in the enclosure for both approaches, with the exception of zebra, whose density was underestimated. The photogrammetry approach offers an alternative approach for deriving camera‐animal observation distances and is particularly useful for application in open habitats, with little occlusion of animals.
Generalized Commuting Graph of Dihedral, Semi-dihedral and Quasi-dihedral Groups
Authors: El-Sanfaz Mustafa Anis , Sarmin Nor Haniza , Zamri Siti Norziahidayu Amzee
Published: January 2022

Commuting graphs are characterized by vertices that are non-central elements of a group where two vertices are adjacent when they commute. In this paper, the concept of commuting graph is extended by defining the generalized commuting graph. Furthermore, the generalized commuting graph of the dihedral groups, the quasi-dihedral groups and the semi-dihedral groups are presented and discussed. The graph properties including chromatic and clique numbers are also explored.
Effect of Bee Bread on Pregnancy Outcomes and Reproductive System of Rats under Heat Stress Exposure
Authors: Mohd Nor Nur Akmar Nadhirah , Komilus Connie Fay , Haron Mohd Nizam , Lananan Fathurrahman , Hou Chew Ha , Yaakub Nadzifah , Yaakub Nadzifah , Kari Asmad
Published: January 2022

Exposure to extreme temperature during pregnancy was associated with abnormal birth outcomes including preterm birth, low birth weight, and placental abortion. Bee bread is a natural product created by bees that is highly nutritional and was recommended for human consumption as a source of high energy and protein. Hence, this study aims to determine the effect of bee bread on pregnancy outcomes and the reproductive system of the ovary and uterus in rats exposed to heat stress.
Nitrogen Tailored Activated Carbon via Microwave Synthesis Method for High Removal of Hydrogen Sulfide
Authors: Mohamad Nor Norhusna , Lee Chung Lau , Mohamed Abdul Rahman
Published: January 2022

In this work, commercialized palm shell activated carbon was modified into nitrogen-functionalized carbon via urea impregnation method, followed by heat treatment via microwave irradiation at 950 °C.
Morphology and Anatomy of Leaf, Stem and Petiole of Luvunga crassifolia Tanaka (Rutaceae)
Authors: Shunmugam Sugathini , Rosli Nur Syamilah , Manickam Sugumaran , Mohd Yusoff Nur Fatihah , Alitheen Noorjahan Banu , Namasivayam Parameswari
Published: January 2022

Luvunga crassifolia is an underutilized plant in the Citrus family. Other than brief morphological descriptions, there are no published reports on other identification features of this plant. Thus, the current study was aimed to investigate macroscopic and microscopic diagnostic features of L. crassifolia leaves, stems, and petioles. Macroscopic characterization, optimization of histological procedure, and histochemical analyses of differential stains were carried out on the leaves, stems, and petioles of L. crassifolia. The histological method was optimized by modifying the following parameters: number of fixation days, dehydration duration with degraded series of ethanol or butanol, clearing duration, and infiltration duration. After infiltration, embedding and sectioning of the tissues were performed. Histochemical analyses were carried out using differential stains to identify the cellular components in leaf, stem and, petiole tissue sections. This study showed that L. crassifolia leaves are amphistomatic. Pellucid dots were observed on both adaxial and abaxial leaf surfaces. Secretory cavities, xylem, phloem, and pericyclic fibers were found in the cross-sections of leaf, stem, and petiole. Calcium oxalates were present in the leaf and stem sections, while trichomes were detected in stem and petiole sections. The information obtained from this study will be helpful for the identification and future taxonomic-related studies of this plant species.
Optimization of flexo process parameters to reduce the overall manufacturing cost
Authors: Joshi Akshay V
Published: January 2022

The flexo process parameters play an important role in ink transfer and will lead to wastage of inks, substrate, solvents and printed stocks if not monitored and controlled. The work focuses on optimizing the flexo process parameters for 40 microns 3-layer polyethylene (PE) film with Blue Nitrocellulose (NC) ink to reduce overall manufacturing cost while maintaining the print quality for diaper application. An experimental design was conducted for the response Ink GSM (grams per square meter), ?E and Print Mottle with factors such as ink viscosity, anilox volume, plate dot shape and substrate opacity. The data was analyzed through Main Effect, Interaction Plot and Analysis of Variance (ANOVA). The regression models were developed for the response to validate the predictive ability of model. The process optimization resulted in reduction of Ink GSM, ?E and Print Mottle by 18%, 52% and 1% respectively. The ink consumption reduced by 18.26% with minimized print defects, thereby reducing the overall manufacturing cost.
Biosorption of Cadmium by fungi isolated from Bharalu river, Assam
Authors:   Department of Molecular Biology and Biotechnology, Cotton University, Guwahati, Assam-781001, India, Deka Dipannita , Bora Pinky ,   Department of Molecular Biology and Biotechnology, Cotton University, Guwahati, Assam-781001, India, Nirjanta Devi Nameirakpam ,   Department of Molecular Biology and Biotechnology, Cotton University, Guwahati, Assam-781001, India, Chabukdhara Mayuri ,   Department of Molecular Biology and Biotechnology, Cotton University, Guwahati, Assam-781001, India
Published: January 2022

Heavy metal pollution in the aquatic ecosystem poses a serious threat to the human health and aquatic biodiversity around. There is urgent need to remediate heavy metals contaminated wastewater through eco friendly ways. Fungi and other microorganisms have been reported to have promising potential to remove heavy metals from wastewater through biosorption. Thus the present work aimed to isolate tolerant fungal species from different sites of a polluted river Bharalu in Assam. After preliminary screening, out of a total of 15 fungal isolates obtained, 4 isolates Aspergillus niger, Aspergillus flavus, Aspergillus fumigates and Colletotrichum gloeosporioides were selected for further study. Tolerance limit of the isolates for Cadmium (Cd) was carried out at concentrations ranging from 100 ppm to 1000 ppm. Results showed that the maximum tolerance was observed in Colletotrichum gloeosporioides (approx. 8.8 mm), followed by Aspergillus flavus (approx. 5.8 mm) at 400ppm. The biosorption efficiency at 400ppm revealed that the maximum Cd concentration was absorbed by fungal biomass of Colletotrichum gloeosporioides (12.83 mg/g) and the minimum by Aspergillus niger (3.91 mg/g). Molecular identification was carried out followed by PCR amplification of the fungal biomass showing highest absorption. The sequence obtained was submitted in the GenBank using BANkIt with accession number-MN714368 which showed high similarities with Colletotrichum gloeosporioides. This results indicated that fungus are promising and potential sources for metal biosorption and detoxification.
On Fat Clothes: Unraveling Plus-Size Design Discourse
Authors: Peters Lauren Downing
Published: January 2022

This article considers the possibilities and limitations of plus-size clothing— a subcategory of ready-to-wear that is deeply embedded in the history of dieting, exercise, standardized sizing, and the industrialization of clothing manufacturing in the United States. In doing so, it draws on fashion theory and disability theory in exposing how plus-size clothing functions as a normalizing mechanism, thereby inhibiting innovation in this sector. The article concludes with a counterexploration of the possibilities of “fat clothes” and the novel w ays of seeing and existing in the world that they might enable.
Problematizer Design: A Foucaultian Approach
Authors: Najar Rodrigo
Published: January 2022

Based on a line of inquiry initiated by Dorst, this article explores Foucault's work as a philosophical inspiration for design research and practice. In terms of foucaultian problematization, notions of discourse and problematization— instead of notions of design problems— is an alternative way of dealing with design situations. It is argued that through the problematization of the discourses interwoven in a design project, the designer takes on a critical and political dimension of their own work. In this way, through the project, designers can have the option to critically choose between reinforcing discourses— in case of agreement with them, or subverting discourses— in case of disagreement.
Flexible Environments for Hybrid Collaboration: Redesigning Virtual Work Through the Four Orders of Design
Authors: Meluso John , Johnson Susan , Bagrow James
Published: January 2022

The COVID-19 pandemic made visceral for many the fact that virtual forms of collaboration— simultaneously liberating and frustrating—are here to stay. Workers’ frustrations demonstrate that challenges remain for work and its design in increasingly “hybrid” collaboration— work in which some people, interacting face-to-face, are co-located while others with whom they work are remote. Using Buchanan's four orders of design, in conjunction with management and information systems scholarship, we present a framework for improving these virtual forms of collaboration. In this article, we review the latest knowledge from these disciplines on virtual collaboration through the lens of the four orders of design. In doing so, we demonstrate that conceiving of work in terms of flexible collaborative environments could increase the unity of purpose between work and workers by leveraging the capabilities of varying degrees of virtuality to engender experiences that benefit all those who interact with work systems.
The Screening and Identification of Key Biomarkers in Adrenocortical Carcinoma: Evidence from a Bioinformatics Analysis
Authors: Yan Xin , Liang Chunfeng , Liang Xinghuan , Li Li , Huang Zhenxing , Yang Haiyan , Qin Yingfen , Lu Decheng , Ma Yan , Luo Zuojie
Published: January 2022

Objective:
 This study aimed to identify the potential key genes associated with the progression and prognosis of adrenocortical carcinoma (ACC).

Methods:
 Differentially expressed
genes (DEGs) in ACC cells and normal adrenocortical cells were assessed by microarray from the Gene Expression Omnibus database. The biological functions of the classified DEGs were examined by Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes pathway (KEGG) enrichment analyses
and a protein–protein interaction (PPI) network was mapped using Cytoscape software. MCODE software was also used for the module analysis and then 4 algorithms of cytohubba software were used to screen hub genes. The overall survival (OS) examination of the hub genes was then performed
by the ualcan online tool.

Results:
 Two GSEs (GSE12368, GSE33371) were downloaded from GEO including 18 and 43 cases, respectively. One hundred and sixty-nine DEGs were identified, including 57 upregulated genes and 112 downregulated
genes. The Gene Ontology (GO) analyses showed that the upregulated genes were significantly enriched in the mitotic cytokines is, nucleus and ATP binding, while the downregulated genes were involved in the positive regulation of cardiac muscle contraction, extracellular space, and heparin-binding
(P < 0.05). The Kyoto Encyclopedia of Genes and Genomes pathway (KEGG) pathway examination showed significant pathways including the cell cycle and the complement and coagulation cascades. The protein– protein interaction (PPI) network consisted of 162 nodes and 847 edges, including
mitotic nuclear division, cytoplasmic, protein kinase binding, and cell cycle. All 4 identified hub genes (FOXM1, UBE2C, KIF11, and NDC80) were associated with the prognosis of adrenocortical carcinoma (ACC) by survival analysis.

Conclusions:

The present study offered insights into the molecular mechanism of adrenocortical carcinoma (ACC) that may be beneficial in further analyses.
Silent Information Regulator 1 (SIRT1) Promotes Pancreatic β-Cell Mitochondrial Autophagy and Pyrin Domains-Containing Protein 3 (NLRP3) Activation Under High Glucose Environment
Authors: Zhang Yang , Sun Peng , Han Shuying , Fan Duojiao
Published: January 2022

Mitochondrial autophagy and inflammatory response involves in diabetes. This study mainly explores the role of Silent Information Regulator (SIRT1) in pancreatic β-cells under high glucose conditions and related mechanism. Pancreatic β cells was cultured in a
high-glucose environment with SRT1720 and EX527 respectively to define activation group and inhibition group followed by analysis of SIRT1, P-FOXO1, FOXO1, LC3, ATG5, PINK, Parkin, Mfn1, Mfn2, Fis1, IL-6, TNF-α, NLRP3 protein and mRNA expression by qRT-PCR, Western blot and fluorescent
probe technology. Compared with control group, SIRT1 protein and mRNA expression in the high glucose group was significantly reduced. Activation group had highest protein and mRNA expression of SIRT1 P-FOXO1, FOXO1, Mfn1, Mfn2, Fis1, PINK, Parkin and mitochondrial membrane potential followed
by blank group and inhibition group.SIRT1 secretion by pancreatic β-cells under high glucose environment is reduced. After activating SIRT1, mitochondrial autophagy decreased significantly and inflammatory response is significantly alleviated, indicating that SIRT1 might be used
as a therapeutic target.
Effect of Thymosin β4 on Deep Second-Degree Scald Wound Healing in Rats via Wnt/β-Catenin Pathway
Authors: Li Shusong , Ma Ying , Liu Zhuoran , Zhao Xiaoyu , Li Li , Wu Xiaoming
Published: January 2022

Objective:
 The purpose of this research is to explore the influences of thymosin β4 (Tβ4) in deepsecond-degree scald wound healing of rat skin and its relationship with Wnt/β-catenin pathway.

Methods:
 Deep second-degree scalded model rats were prepared and divided into normal saline (NS) treatment group, Tβ4 treatment group and FH535 inhibitor group. Then, the concentrations of inflammatory factors in the rats were monitored
via adopting the correlated TNF-α and IL-1β ELISA kits. In the meantime, the wound healing rate was analyzed via photography. Subsequently, the qRTPCR procedure was wielded to determine Wnt1 and β-catenin expression in wound tissues, and the degree of wound
tissue injury was examined via hematoxylin and eosin (HE) staining. Finally, Western blotting (WB) was adopted to assess Wnt/β-catenin pathway-associated protein levels.

Results:
 Releasing amount of TNF-α
and IL-1β were conspicuously up-regulated after scalding (p <0.01), and Wnt1 and β-catenin expression at molecular transcription level was also significantly raised (p < 0.01). Besides, treatment with 18 μg of Tβ4 significantly
increased the wound healing rate of scalded rats (p < 0.01). In addition, Tβ4 treatment significantly promoted wound healing (p < 0.01) and increased the Wnt1 and β-catenin expression levels (p < 0.01). Moreover, FH535 significantly restrained
the Wnt/β-catenin pathway-correlated protein levels (p < 0.01) and wound healing.

Conclusion:
 Tβ4 can promote scald wound healing in rats and may play a role via evoking Wnt/β-catenin
pathway activation.
Alleviation of Papain-Induced Osteoarthritis by Recombinant Human Endostatin via Downregulation of Matrix Metalloproteinase-13, Interleukin-1 and Interleukin-6 in Rats
Authors: Ou Chunpei , Chen Pengfei , Song Jinqi , Deng Xuefeng , Chen Feiqiang , Hong Xiexi , Zhang Xiangrong
Published: January 2022

Osteoarthritis (OA) is a degenerative disease of joints commonly occurring in the elderly and middleaged people. This study aimed to investigate the effect of recombinant human endostatin (rhEndo) on OA and the levels of MMP-13, IL-1 and IL-6 in the synovial fluid in osteoarthritis
rats. OA models were made by injecting 4% papain into the knee joint cavity of rats once every three days for three times. The models were then injected subcutaneously with rhEndo and examined six weeks later for the Mankin scores and levels of MMP-13, IL-1 and IL-6 using ELISA. Compared with
control, the Mankin score as well as the levels of IL-1, IL-6 and MMP-13 were significantly increased in the models (0.30 vs. 5.80, 1.12 vs. 12.84 pg/ mL, 12.22 vs. 43.82 pg/ mL and 0.23 vs. 26.31 ng/ mL). Following treatment with 4 mg/kg rhEndo, the Mankin score in model decreased to 0.90,
meanwhile, the levels of IL-1, IL-6 and MMP-13 decreased significantly to 0.79 pg/ mL, 2.89 pg/mL and 1.17 ng/mL, respectively, in a dose dependent manner. Therefore, rhEndo can alleviate osteoarthritis by reducing MMP-13, IL-1 and IL-6 expression in rats.
Up-Regulation of miR-1925 by Bone Marrow Mesenchymal Stem Cell (BMSC) Inhibits the Growth of Liver Cancer by Promoting the Anti-Tumor Activity of Natural Killer (NK) Cells
Authors: Ding Chencheng , Zheng Yunjie , Li Dan , Zhu Min , Zhu Yong
Published: January 2022

Hepatocellular carcinoma (HCC) seriously threatens human health and life quality. Natural killer (NK) cells play important roles in liver immune function. Bone marrow mesenchymal stem cell (BMSC) exosomes (Exo) participate in tissue damage. This study explored BMSC-Exo’s effect
on NK cells’ anti-tumor activity. NK cells were isolated from the livers of mice with liver cancer. NK cells with or without BMSC-Exo treatment were co-cultured with liver cancer cells to assess cell proliferation. Administration of BMSC-Exo into mice with liver cancer significantly
suppressed liver cancer cell growth. In addition, BMSC-Exo treatment significantly improved NK cells’ anti-tumor effect whic was related to BMSC-Exo-induced up-regulation of miR-1925. Implantation of BMSC-Exo into mice with liver cancer at different time periods can significantly suppress
liver cancer cell growth. At the same time, BMSC-Exo implantation inhibited the expression of cell proliferation marker protein(Ki67). In vitro study found that BMSC-Exo treatment significantly increased miR-1925 level and the toxicity of NK cells to HCC cells. In addition, miR-1925
overexpression in NK cells significantly increased NK cells’ anti-tumor activity. In conclusion, this study proved that up-regulation of miR-1925 by BMSC can inhibit the growth of liver cancer by promoting the anti-tumor activity of NK cells.
The Effect of Bone Marrow Mesenchymal Stem Cells (BMSCs) on Brain Injury Repair and Synapse Regeneration in Mice Under Different Conditions of Intrauterine Ischemia and Hypoxia Through Wnt Pathway
Authors: Fu Changtao , Zhou Youdong , Wang Lei
Published: January 2022

Bone marrow mesenchymal stem cells (BMSCs) can be differentiated into a variety of cells and repair damaged cells. We explore whether BMSCs can repair brain damage and synapses regeneration in mice under intrauterine ischemia and hypoxia. Twenty-five pregnant mice were assigned into
control group, 6% hypoxic injury group, 8% hypoxic injury group, 6% treatment group, 8% treatment group followed by analysis of the expression of MBP, MAG, CSPGs, IGF-1, NCAN, COLIV, SynD1G1, GFAP, GSK-3β, and β-actin by RT-PCR and Western blot. Our results showed that
the expression of MBP, MAG, COL IV, SynD1G1, IGF-1 in the treatment group were significantly higher than those in hypoxic injury group with significant differences between the 8% treatment group and 6% treatment group (P < 0.05). In conclusion, BMSCs can repair brain damage and synapse
regeneration in mice under different intrauterine ischemia and hypoxia conditions which might be through Wnt signaling pathway.
Icariin Promotes In Vitro Cardiomyocyte Proliferation and Differentiation in Human Bone Marrow-Derived Mesenchymal Stem Cells
Authors: Liu Shaoying , Zhang Chengying , Hao Jing , Liu Yuna , Zheng Sidao , Yang Cui , Yang Jiyuan , Wu Hongjin
Published: January 2022

Mesenchymal stem cells (MSCs) are the excellent candidates in myocardial regeneration given their easy accessibility, low immunogenicity and high potential for cardiomyocyte differentiation. This work focused on investigating the role of icariin, a main active component of the Traditional
Chinese herb epimedium, in human bone marrow-derived MSCs (BMSCs) proliferation and differentiation into cardiomyocytes In Vitro. Human BMSCs were cultivated In Vitro, and MTT assay was conducted to measure their proliferation. On this basis, we selected the optimal icariin dose
for promoting the proliferation to induce cardiomyocyte differentiation of MSCs, which were pretreated with or without 5-azacytidine (5-Aza). Cardiac-specific cardiac troponin I (cTnI) and connexin 43 (Cx43)-positive cells were detected by immunofluorescent staining. The differentiation ratio
of MSCs was examined by flow cytometry. This study measured early cardiac transcription factors (TFs) Nkx2.5 and GATA4 levels through RT-PCR and Western blotting (WB). As a result, icariin increased MSC proliferation dependent on its dose, and the optimal dose was determined to be 80 μg/l.
Furthermore, MSCs showed minimal cardiomyogenic differentiation when induced by icariin alone as confirmed by the expression of cardiac-related markers. Moreover, a synergic interaction was observed when icariin and 5-Aza cooperated to induce cardiomyocyte differentiation of MSCs. In conclusion,
Icariin stimulates proliferation and facilitates cardiomyocyte differentiation of MSCs In Vitro and may be potentially used as a new method for enhancing the MSCs efficacy in cardiovascular disease.
Bone Marrow Mesenchymal Stem Cells (BMSCs) Restrain the Malignant Behaviors of A549 Lung Cancer Cells Under Hypoxia via miR-145
Authors: Song Haibin , Zhang Heng , Li Lei
Published: January 2022

Deriving from bone marrow, the bone marrow mesenchymal stem cells (BMSCs) possess multipolar chemotaxis, proliferation potential, along with the capability to differentiate into various types of cells. Moreover, the hypoxic stimulation can effectively induce BMSCs differentiation. This
study intends to explore the impediment of BMSCs on malignant behaviors of lung cancer stem cells under hypoxia. A co-culture system of BMSCs with A549 cells was established and then assigned into normoxia group, hypoxia group (50, 100, and 200 nmol/L) followed by analysis of cell viability
by CCK-8 assay and miR-145 expression by qRT-PCR. In addition, A549 cells were grouped into NC group, miR-145-mimics group, and miR-145-inhibitors group followed by analysis of cell invasion and levels of miR-145 and Oct4. Hypoxia group exhibited a reduced cell viability and higher miR-145
expression (146.01±21.23%) compared to normoxia group (P < 0.05). Transfection of miR-145-mimic significantly upregulated miR-145 and decreased cell invasion (7.49±1.43%) compared with miR-145-inhibitors group or NC group (P < 0.05). Meanwhile, Oct4 level
in miR-145-mimics group (0.934±2.98) was significantly decreased (P < 0.05). In conclusion, under hypoxia condition, the co-culture with BMSCs can upregulated miR-145 level, effectively reduce the viability of lung cancer stem cells and restrain proliferation capability.
Down-Regulation of p38 Mitogen-Activated Protein Kinases/Nuclear Factor Kappa Light Chain Enhancer of Activated B Cells (p38 MAPK/NF-κB) Signaling Pathway Promotes Bone Marrow Mesenchymal Stem Cells Differentiation into Neural Stem Cells in Healing Neurodegeneration
Authors: Yang Xin , Wang Shandan
Published: January 2022

This study intends to promote bone marrow mesenchymal stem cells (BMSCs) differentiation into neural stem cells by down-regulating p38 MAPK/NF-κB to heal neurodegeneration. 26 patients with neurodegenerative diseases were enrolled from the Department of Neurology along
with recruitment of 26 other healthy controls followed by analysis of p38 MAPK/NF-κB signaling pathway expression by ELISA. BMSCs were cultured and characterized by flow cytometry. Western blot and qRTPCR measured the p38 MAPK/NF-κB expression in the absence or presence
of p38 MAPK/NF-κB inhibitors. p38 MAPK/NF-κB expression in 26 neurodegenerative patients was significantly higher than that of 26 healthy controls. The qRT-PCR and western blot results showed that the neural stem cell-specific proteins expression was increased as
days went; after addition of p38 MAPK/NF-κB inhibitor, the expression of related specific genes were significantly decreased. In conclusion, inhibition of the expression of p38 MAPK/NF-κB signaling pathway can heal neurodegeneration by promoting the differentiation
of BMSCs into neural stem cells.