Transfection types, methods and strategies: a technical review
Transfection is a modern and powerful method used to insert foreign nucleic acids into eukaryotic cells. The ability to modify host cells’ genetic content enables the broad application of this process in studying normal cellular processes, disease molecular mechanism and gene therapeutic effect. In this review, we summarized and compared the findings from various reported literature on the characteristics, strengths, and limitations of various transfection methods, type of transfected nucleic acids, transfection controls and approaches to assess transfection efficiency. With the vast choices of approaches available, we hope that this review will help researchers, especially those new to the field, in their decision making over the transfection protocol or strategy appropriate for their experimental aims.
Chong et al. (2021) Transfection types, methods and strategies: a technical review. PeerJ 9:e11165 https://doi.org/10.7717/peerj.11165
Genome-wide identification and expression analysis of the EXO70 gene family in grape (Vitis vinifera L)
EXO70 is the pivotal protein subunit of exocyst, which has a very crucial role in enhancing the shielding effect of the cell wall, resisting abiotic and hormonal stresses. This experiment aims to identify family members of the EXO70 gene family in grape and predict the characteristics of this gene family, so as to lay the foundation of further exploring the mechanism of resisting abiotic and hormone stresses of VvEXO70s. Therefore, the Vitis vinifera ‘Red Globe’ tube plantlet were used as materials. Bioinformatics was used to inquire VvEXO70 genes family members, gene structure, system evolution, cis-acting elements, subcellular and chromosomal localization, collinearity, selective pressure, codon bias and tissue expression. All of VvEXO70s had the conserved pfam03081 domain which maybe necessary for interacting with other proteins. Microarray analysis suggested that most genes expressed to varying degrees in tendrils, leaves, seeds, buds, roots and stems. Quantitative Real-Time PCR (qRT-PCR) showed that the expression levels of all genes with 5 mM salicylic acid (SA), 0.1 mM methy jasmonate (MeJA), 20% PEG6000 and 4 °C for 24 h were higher than for 12 h. With 20% PEG6000 treatment about 24 h, the relative expression of VvEXO70-02 was significantly up-regulated and 361 times higher than CK. All genes’ relative expression was higher at 12 h than that at 24 h after treatment with 7 mM hydrogen peroxide (H2O2) and 0.1 mM ethylene (ETH). In conclusion, the expression levels of 14 VvEXO70 genes are distinguishing under these treatments, which play an important role in the regulation of anti-stress signals in grape. All of these test results provide a reference for the future research on the potential function analysis and plant breeding of VvEXO70 genes.
Wang et al. (2021) Genome-wide identification and expression analysis of the EXO70 gene family in grape (Vitis vinifera L). PeerJ 9:e11176 https://doi.org/10.7717/peerj.11176
Chemosensitivity and role of swimming legs of mud crab, Scylla paramamosain, in feeding activity as determined by electrocardiographic and behavioural observations
Swimming crabs have a characteristic fifth pair of legs that are flattened into paddles for swimming purposes. The dactyl of these legs bears a thick seta along its edge. The chemoreceptive and feeding properties of the seta are supported with scientific evidence; however, there is no available data on the sensitivity of the setae in portunid crabs. The underlying mechanisms of the chemo- and mechano-sensitivity of appendages and their involvement in feeding activities of the mud crab (Scylla paramamosain) were investigated using electrocardiography and behavioural assay, which focused on the responses of the mud crab to chemical and touch stimulus. Electrocardiography revealed the sensory properties of the appendages. The dactyls of swimming legs and the antennules were chemosensitive, but not mechanosensitive and vice versa for the antennae. However, the mouthparts, claws, and walking legs were chemo- and mechanosensitive. Only the chemosensitive appendages, including the swimming legs, were directly involved in feeding. The flattened dactyls of the swimming legs were more efficient than the pointed dactyls of the walking legs in detecting the food organism crawling on the substrate. The structural features enhanced the capacity of the crab in coming into contact with scattered food items. This study revealed that the swimming legs are important appendages for feeding in the mud crab.
Kawamura et al. (2021) Chemosensitivity and role of swimming legs of mud crab, Scylla paramamosain, in feeding activity as determined by electrocardiographic and behavioural observations. PeerJ 9:e11248 https://doi.org/10.7717/peerj.11248
First remains of the enormous alligatoroid Deinosuchus from the Upper Cretaceous Menefee Formation, New Mexico
The neosuchian Deinosuchus is known from numerous localities throughout the Campanian of North America, from New Jersey to Montana (USA) and as far south as Coahuila (Mexico). Here we describe six osteoderms, two vertebrae, and a partial tooth discovered in the Menefee Formation of New Mexico and assign them to Deinosuchus sp., representing one of the earliest occurrences of this genus on the Laramidian subcontinent, and among the earliest known occurrences of this large alligatoroid in all of North America. The osteoderms are morphologically distinct in their inflated construction, with deep and radially distributed pitting, which closely matches osteoderms of Deinosuchus.
Mohler et al. (2021) First remains of the enormous alligatoroid Deinosuchus from the Upper Cretaceous Menefee Formation, New Mexico. PeerJ 9:e11302 https://doi.org/10.7717/peerj.11302
Association between body mass index and blood pressure levels across socio-demographic groups and geographical settings: analysis of pooled data in Peru
Background Understanding the relationship between BMI and blood pressure requires assessing whether this association is similar or differs across population groups. This study aimed to assess the association between body mass index (BMI) and blood pressure levels, and how these associations vary between socioeconomic groups and geographical settings. Methods Data from the National Demographic Health Survey of Peru from 2014 to 2019 was analyzed considering the complex survey design. The outcomes were levels of systolic (SBP) and diastolic blood pressure (DBP), and the exposure was BMI. Exposure and outcomes were fitted as continuous variables in a non-linear quadratic regression model. We explored effect modification by six socioeconomic and geographical variables (sex, age, education level, socioeconomic position, study area, and altitude), fitting an interaction term between each of these variables and BMI. Results Data from 159, 940 subjects, mean age 44.4 (SD: 17.1), 54.6% females, was analyzed. A third (34.0%) of individuals had ≥12 years of education, 24.7% were from rural areas, and 23.7% lived in areas located over 2,500 m above sea level. In the overall sample mean BMI was 27.1 (SD: 4.6) kg/m2, and mean SBP and DBP were 122.5 (SD: 17.2) and 72.3 (SD: 9.8) mmHg, respectively. In the multivariable models, greater BMI levels were associated with higher SBP (p-value < 0.001) and DBP (p-value < 0.001). There was strong evidence that sex, age, education level, and altitude were effect modifiers of the association between BMI and both SBP and DBP. In addition to these socio-demographic variables, socioeconomic position and study area were also effect modifiers of the association between BMI and DBP, but not SBP. Conclusions The association between BMI and levels of blood pressure is not uniform on a range of socio-demographic and geographical population groups. This characterization can inform the understanding of the epidemiology and rise of blood pressure in a diversity of low-resource settings.
Bernabe-Ortiz et al. (2021) Association between body mass index and blood pressure levels across socio-demographic groups and geographical settings: analysis of pooled data in Peru. PeerJ 9:e11307 https://doi.org/10.7717/peerj.11307
Fast computational mutation-response scanning of proteins
Studying the effect of perturbations on protein structure is a basic approach in protein research. Important problems, such as predicting pathological mutations and understanding patterns of structural evolution, have been addressed by computational simulations that model mutations using forces and predict the resulting deformations. In single mutation-response scanning simulations, a sensitivity matrix is obtained by averaging deformations over point mutations. In double mutation-response scanning simulations, a compensation matrix is obtained by minimizing deformations over pairs of mutations. These very useful simulation-based methods may be too slow to deal with large proteins, protein complexes, or large protein databases. To address this issue, I derived analytical closed formulas to calculate the sensitivity and compensation matrices directly, without simulations. Here, I present these derivations and show that the resulting analytical methods are much faster than their simulation counterparts.
Echave (2021) Fast computational mutation-response scanning of proteins. PeerJ 9:e11330 https://doi.org/10.7717/peerj.11330
Widely assumed phenotypic associations in Cannabis sativa lack a shared genetic basis
The flowering plant Cannabis sativa, cultivated for centuries for multiple purposes, displays extensive variation in phenotypic traits in addition to its wide array of secondary metabolite production. Notably, Cannabis produces two well-known secondary-metabolite cannabinoids: cannabidiolic acid (CBDA) and delta-9-tetrahydrocannabinolic acid (THCA), which are the main products sought by consumers in the medical and recreational market. Cannabis has several suggested subspecies which have been shown to differ in chemistry, branching patterns, leaf morphology and other traits. In this study we obtained measurements related to phytochemistry, reproductive traits, growth architecture, and leaf morphology from 297 hybrid individuals from a cross between two diverse lineages. We explored correlations among these characteristics to inform our understanding of which traits may be causally associated. Many of the traits widely assumed to be strongly correlated did not show any relationship in this hybrid population. The current taxonomy and legal regulation within Cannabis is based on phenotypic and chemical characteristics. However, we find these traits are not associated when lineages are inter-crossed, which is a common breeding practice and forms the basis of most modern marijuana and hemp germplasms. Our results suggest naming conventions based on leaf morphology do not correspond to the chemical properties in plants with hybrid ancestry. Therefore, a new system for identifying variation within Cannabis is warranted that will provide reliable identifiers of the properties important for recreational and, especially, medical use.
Vergara et al. (2021) Widely assumed phenotypic associations in Cannabis sativa lack a shared genetic basis. PeerJ 9:e10672 https://doi.org/10.7717/peerj.10672
Negative psychological aspects of working with experimental animals in scientific research
The aim of the study was to reveal the negative psychological aspects of using animals by scientists and to determine whether the emotional tensions and stress are associated with performing experiments on animals. All 150 participants of the study conduct experiments on animals in their work. Computer-assisted web interviewing, was used to collect the data. Correlation matrices for factorial analysis of main component loads and cluster analysis have been calculated as grouping methods revealed two different categories of researchers, which were mostly distinguished by acceptance and aversion to animal testing and animal welfare. The main findings demonstrated, that there is a group of respondents who feel discomfort when performing experiments on animals. Especially young people involved in animal testing, feel remorse, emotional tension and helplessness.
Mamzer et al. (2021) Negative psychological aspects of working with experimental animals in scientific research. PeerJ 9:e11035 https://doi.org/10.7717/peerj.11035
Prevalence of depression and its impact on quality of life in frontline otorhinolaryngology nurses during the COVID-19 pandemic in China
Objective Exposure to the coronavirus disease 2019 (COVID-19) was associated with high risk of mental health problems among frontline nurses. This study examined the prevalence of depressive symptoms (depression hereafter) and its impact on quality of life (QOL) in otorhinolaryngology (ENT) nurses during the COVID-19 pandemic in China. Methods An online study was conducted between March 15 and March 20, 2020. Depression and QOL were assessed using standardized instruments. Results A total of 1,757 participants were recruited. The prevalence of depression was 33.75% (95% CI: 31.59%-35.97%). Results emerging from multiple logistic regression analysis showed that direct care of COVID-19 patients (OR: 1.441, 95% CI: 1.031–2.013, P = 0.032), and current smoking (OR: 2.880, 95% CI: 1.018–8.979, P = 0.048) were significantly associated with depression. After controlling for covariates, ENT nurses with depression had a lower overall QOL compared to those without depression (F(1, 1757)= 536.80, P < 0.001). Conclusions Depression was common among ENT nurses during the COVID-19 pandemic in China. Considering the negative impact of depression on QOL and care quality, regular screening for depression should be conducted in ENT nurses and treatment should be provided.
Tian et al. (2021) Prevalence of depression and its impact on quality of life in frontline otorhinolaryngology nurses during the COVID-19 pandemic in China. PeerJ 9:e11037 https://doi.org/10.7717/peerj.11037
Epidemiology of antimicrobial resistance (AMR) on California dairies: descriptive and cluster analyses of AMR phenotype of fecal commensal bacteria isolated from adult cows
Background This study describes the occurrence of antimicrobial resistance (AMR) in commensal Escherichia coli and Enterococcus/Streptococcus spp. (ES) isolated from fecal samples of dairy cows and assesses the variation of AMR profiles across regions and seasons following the implementation of the Food and Agricultural Code (FAC) Sections 14400–14408 (formerly known as Senate Bill, SB 27) in California (CA). Methods The study was conducted on ten dairies distributed across CA’s three milk sheds: Northern California (NCA), Northern San Joaquin Valley (NSJV), and the Greater Southern California (GSCA). On each study dairy, individual fecal samples were collected from two cohorts of lactating dairy cows during the fall/winter 2018 and spring/summer 2019 seasons. Each cohort comprised of 12 cows per dairy. The fecal samples were collected at enrollment before calving (close-up stage) and then monthly thereafter for four consecutive time points up to 120 days in milk. A total of 2,171 E. coli and 2,158 ES isolates were tested for antimicrobial susceptibility using the broth microdilution method against a select panel of antimicrobials. Results The E. coli isolates showed high resistance to florfenicol (83.31% ± 0.80) and sulphadimethoxine (32.45%), while resistance to ampicillin (1.10% ± 0.21), ceftiofur (1.93% ± 0.29), danofloxacin (4.01% ± 0.42), enrofloxacin (3.31% ± 0.38), gentamicin (0.32% ± 0.12) and neomycin (1.61% ± 0.27) had low resistance proportions. The ES isolates were highly resistant to tildipirosin (50.18% ± 1.10), tilmicosin (48% ± 1.10), tiamulin (42%) and florfenicol (46% ± 1.10), but were minimally resistant to ampicillin (0.23%) and penicillin (0.20%). Multidrug resistance (MDR) (resistance to at least 1 drug in ≥3 antimicrobial classes) was observed in 14.14% of E. coli isolates and 39% of ES isolates. Escherichia coli isolates recovered during winter showed higher MDR prevalence compared to summer isolates (20.33% vs. 8.04%). A higher prevalence of MDR was observed in NSJV (17.29%) and GSCA (15.34%) compared with NCA (10.10%). Conclusions Our findings showed high rates of AMR to several drugs that are not labeled for use in lactating dairy cattle 20 months of age or older. Conversely, very low resistance was observed for drugs labeled for use in adult dairy cows, such as cephalosporins and penicillin. Overall, our findings identified important differences in AMR by antimicrobial class, region and season.
Abdelfattah et al. (2021) Epidemiology of antimicrobial resistance (AMR) on California dairies: descriptive and cluster analyses of AMR phenotype of fecal commensal bacteria isolated from adult cows. PeerJ 9:e11108 https://doi.org/10.7717/peerj.11108