title: PeerJ
description:  Articles published in PeerJ
link: https://peerj.com/articles/index.rss3?journal=peerj&page=369
creator: info@peerj.com PeerJ
errorsTo: info@peerj.com PeerJ
language: en

title: Using transplantation to restore seagrass meadows in a protected South African lagoon
link: https://peerj.com/articles/16500
last-modified: 2023-11-29
description: BackgroundSeagrass meadows provide valuable ecosystem services but are threatened by global change pressures, and there is growing concern that the functions seagrasses perform within an ecosystem will be reduced or lost without intervention. Restoration has become an integral part of coastal management in response to major seagrass declines, but is often context dependent, requiring an assessment of methods to maximise restoration success. Here we investigate the use of different restoration strategies for the endangered Zostera capensis in South Africa.MethodsWe assessed restoration feasibility by establishing seagrass transplant plots based on different transplant source materials (diameter (ø) 10 cm cores and anchored individual shoots), planting patterns (line, dense, bullseye) and planting site (upper, upper-mid and mid-intertidal zones). Monitoring of area cover, shoot length, and macrofaunal diversity was conducted over 18 months.ResultsMixed model analysis showed distinct effects of transplant material used, planting pattern and site on transplant survival and area cover. Significant declines in seagrass cover across all treatments was recorded post-transplantation (2 months), followed by a period of recovery. Of the transplants that persisted after 18 months of monitoring (~58% plots survived across all treatments), seagrass area cover increased (~112%) and in some cases expanded by over >400% cover, depending on type of transplant material, planting arrangement and site. Higher bioturbator pressure from sandprawns (Kraussillichirus kraussi) significantly reduced transplant survival and area cover. Transplant plots were colonised by invertebrates, including seagrass specialists, such as South Africa’s most endangered marine invertebrate, the false-eelgrass limpet (Siphonaria compressa). For future seagrass restoration projects, transplanting cores was deemed the best method, showing higher long-term persistence and cover, however this approach is also resource intensive with potentially negative impacts on donor meadows at larger scales. There is a clear need for further research to address Z. capensis restoration scalability and improve long-term transplant persistence.
creator: Katie M. Watson
creator: Deena Pillay
creator: Sophie von der Heyden
uri: https://doi.org/10.7717/peerj.16500
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2023 Watson et al.

title: Centre of pressure changes during stance but not during gait in young women after alcohol intoxication
link: https://peerj.com/articles/16511
last-modified: 2023-11-29
description: BackgroundWomen are underrepresented in research focused on alcohol (e.g., Brighton, Moxham & Traynor, 2016; DOI 10.1097/JAN.0000000000000136) despite the changing patterns of alcohol consumption, which has been increasing in women in recent decades. The purpose of this study was to analyse the relationship between habitual alcohol consumption and centre of pressure (CoP) parameters during stance and gait while intoxicated by alcohol.MethodsThirty women (24.39 ± 2.93 years) participated in this study. All participants were asked to answer the AUDIT questionnaire. Stance and gait analysis were repeated under two conditions on a Zebris platform (FDM GmbH; Munich, Germany): when the participants were sober (0.00% breath alcohol concentration, BrAC) and when they were in an intoxicated state (0.11% BrAC). Participants were divided by their AUDIT score into a low-risk alcohol consumption group (n = 15; AUDIT score: 3 to 6) and a hazardous alcohol consumption group (n = 15; AUDIT score: 7 to 13).ResultsNo statistical difference was observed in stance and gait parameters when comparing the low-risk and hazardous groups under 0.00% BrAC and 0.11% BrAC conditions. A statistically significant difference was observed when comparing 0.00% BrAC and 0.11% BrAC conditions within each group. This significant difference was found in CoP path length and CoP average velocity during quiet stance. However, no statistically significant differences were observed in CoP parameters during gait. An alcohol intoxication of 0.11% BrAC was not sufficient to cause statistically significant impairments in butterfly parameters of gait.
creator: Marta Gimunová
creator: Michal Bozděch
creator: Jan Novák
uri: https://doi.org/10.7717/peerj.16511
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2023 Gimunová et al.

title: Significant improvement in survival outcomes of trisomy 18 with neonatal intensive care compared to non-intensive care: a single-center study
link: https://peerj.com/articles/16537
last-modified: 2023-11-29
description: BackgroundTrisomy 18 syndrome, also known as Edwards syndrome, is a chromosomal trisomy. The syndrome has historically been considered lethal owing to its poor prognosis, and palliative care was primarily indicated for trisomy 18 neonates. Although there have been several reports on the improvement of survival outcomes in infants with trisomy 18 syndrome through neonatal intensive care, few studies have compared the impact of neonatal intensive care on survival outcomes with that of non-intensive care. Therefore, we compared the survival-related outcomes of neonates with trisomy 18 between intensive and non-intensive care.MethodsSeventeen infants of trisomy 18 admitted to our center between 2007 and 2019 were retrospectively studied. We divided the patients into a non-intensive group (n = 5) and an intensive group (n = 12) and evaluated their perinatal background and survival-related outcomes of the two groups.ResultsThe 1- and 3-year survival rates were both 33% in the intensive group, which was significantly higher than that in the non-intensive group (p < 0.001). Half of the infants in the intensive care group were discharged alive, whereas in the non-intensive care group, all died during hospitalization (p = 0.049).ConclusionsNeonatal intensive care for neonates with 18 trisomy significantly improved not only survival rates but also survival-discharge rates. Our findings would be helpful in providing 18 trisomy neonates with standard neonatal intensive care when discussing medical care with their parents.
creator: Shigeki Koshida
creator: Kentaro Takahashi
uri: https://doi.org/10.7717/peerj.16537
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2023 Koshida and Takahashi

title: A novel long noncoding RNA (lncRNA), LINC02657(LASTR), is a prognostic biomarker associated with immune infiltrates of lung adenocarcinoma based on unsupervised cluster analysis
link: https://peerj.com/articles/16167
last-modified: 2023-11-28
description: Non-small cell lung cancer (NSCLC) has long been the deadliest malignancy worldwide, with adenocarcinoma (AD) being the most common pathological subtype. Here we focused on the value of LASTR in LUAD. Using expression analysis, enrichment analysis, immune cell infraction analysis, we found that the expression level of LASTR was significantly increased in LUAD tissue. Meanwhile, LASTR was significantly associated with differential infiltration of various immune cells. Kaplan-Meier survival analysis showed that LUAD related with a poor prognosis in terms of OS, PFI, and DSS compared with high-expression LASTR. The enrichment analysis showed that LASTR is related to the pathays like PI3K-AKT signaling pathway. Thus, the present findings could be helpful in a better understand of LASTR in LUAD. RT-PCR was used to verify the high expression of LASTR in LUAD tissues, and the apoptosis of LUAD cell lines was promoted by CCK8 and Transwell experiments to verify the ability of LASTR to promote the migration and invasion of lung cancer cells in vitro.
creator: Fanming Kong
creator: Xinyu Yang
creator: Zhichao Lu
creator: Zongheng Liu
creator: Yang Yang
creator: Ziheng Wang
uri: https://doi.org/10.7717/peerj.16167
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2023 Kong et al.

title: An atlas of rational genetic engineering strategies for improved xylose metabolism in Saccharomyces cerevisiae
link: https://peerj.com/articles/16340
last-modified: 2023-11-28
description: Xylose is the second most abundant carbohydrate in nature, mostly present in lignocellulosic material, and representing an appealing feedstock for molecule manufacturing through biotechnological routes. However, Saccharomyces cerevisiae—a microbial cell widely used industrially for ethanol production—is unable to assimilate this sugar. Hence, in a world with raising environmental awareness, the efficient fermentation of pentoses is a crucial bottleneck to producing biofuels from renewable biomass resources. In this context, advances in the genetic mapping of S. cerevisiae have contributed to noteworthy progress in the understanding of xylose metabolism in yeast, as well as the identification of gene targets that enable the development of tailored strains for cellulosic ethanol production. Accordingly, this review focuses on the main strategies employed to understand the network of genes that are directly or indirectly related to this phenotype, and their respective contributions to xylose consumption in S. cerevisiae, especially for ethanol production. Altogether, the information in this work summarizes the most recent and relevant results from scientific investigations that endowed S. cerevisiae with an outstanding capability for commercial ethanol production from xylose.
creator: Beatriz de Oliveira Vargas
creator: Jade Ribeiro dos Santos
creator: Gonçalo Amarante Guimarães Pereira
creator: Fellipe da Silveira Bezerra de Mello
uri: https://doi.org/10.7717/peerj.16340
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2023 Vargas et al.

title: Diversity and ice nucleation activity of Pseudomonas syringae in drone-based water samples from eight lakes in Austria
link: https://peerj.com/articles/16390
last-modified: 2023-11-28
description: Bacteria from the Pseudomonas syringae complex (comprised of at least 15 recognized species and more than 60 different pathovars of P. syringae sensu stricto) have been cultured from clouds, rain, snow, streams, rivers, and lakes. Some strains of P. syringae express an ice nucleation protein (hereafter referred to as ice+) that catalyzes the heterogeneous freezing of water. Though P. syringae has been sampled intensively from freshwater sources in the U.S. and France, little is known about the genetic diversity and ice nucleation activity of P. syringae in other parts of the world. We investigated the haplotype diversity and ice nucleation activity at −8 °C (ice+) of strains of P. syringae from water samples collected with drones in eight freshwater lakes in Austria. A phylogenetic analysis of citrate synthase (cts) sequences from 271 strains of bacteria isolated from a semi-selective medium for Pseudomonas revealed that 69% (188/271) belonged to the P. syringae complex and represented 32 haplotypes in phylogroups 1, 2, 7, 9, 10, 13, 14 and 15. Strains within the P. syringae complex were identified in all eight lakes, and seven lakes contained ice+ strains. Partial 16S rDNA sequences were analyzed from a total of 492 pure cultures of bacteria isolated from non-selective medium. Nearly half (43.5%; 214/492) were associated with the genus Pseudomonas. Five of the lakes (ALT, GRU, GOS, GOL, and WOR) were all distinguished by high levels of Pseudomanas (p ≤ 0.001). HIN, the highest elevation lake, had the highest percentage of ice+ strains. Our work highlights the potential for uncovering new haplotypes of P. syringae in aquatic habitats, and the use of robotic technologies to sample and characterize microbial life in remote settings.
creator: Regina Hanlon
creator: Celia Jimenez-Sanchez
creator: James Benson
creator: Ken Aho
creator: Cindy Morris
creator: Teresa M. Seifried
creator: Philipp Baloh
creator: Hinrich Grothe
creator: David Schmale
uri: https://doi.org/10.7717/peerj.16390
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2023 Hanlon et al.

title: A multicentre study to determine the in vitro efficacy of flomoxef against extended-spectrum beta-lactamase producing Escherichia coli in Malaysia
link: https://peerj.com/articles/16393
last-modified: 2023-11-28
description: BackgroundThe high burden of extended-spectrum beta-lactamase-producing (ESBL)-producing Enterobacterales worldwide, especially in the densely populated South East Asia poses a significant threat to the global transmission of antibiotic resistance. Molecular surveillance of ESBL-producing pathogens in this region is vital for understanding the local epidemiology, informing treatment choices, and addressing the regional and global implications of antibiotic resistance.MethodsTherefore, an inventory surveillance of the ESBL-Escherichia coli (ESBL-EC) isolates responsible for infections in Malaysian hospitals was conducted. Additionally, the in vitro efficacy of flomoxef and other established antibiotics against ESBL-EC was evaluated.ResultsA total of 127 non-repetitive ESBL-EC strains isolated from clinical samples were collected during a multicentre study performed in five representative Malaysian hospitals. Of all the isolates, 33.9% were isolated from surgical site infections and 85.8% were hospital-acquired infections. High rates of resistance to cefotaxime (100%), cefepime (100%), aztreonam (100%) and trimethoprim-sulfamethoxazole (100%) were observed based on the broth microdilution test. Carbapenems remained the most effective antibiotics against the ESBL-EC, followed by flomoxef. Antibiotic resistance genes were identified by PCR. The blaCTX-M-1 was the most prevalent ESBL gene, with 28 isolates (22%) harbouring blaCTX-M-1 only, 27 isolates (21.3%) co-harbouring blaCTX-M-1 and blaTEM, and ten isolates (7.9%) co-harbouring blaCTX-M-1,blaTEM and blaSHV. A generalised linear model showed significant antibacterial activity of imipenem against different types of infection. Besides carbapenems, this study also demonstrated a satisfactory antibacterial activity of flomoxef (81.9%) on ESBL-EC, regardless of the types of ESBL genes.
creator: Polly Soo Xi Yap
creator: Chun Wie Chong
creator: Sasheela Ponnampalavanar
creator: Ramliza Ramli
creator: Azian Harun
creator: Tengku Zetty Maztura Tengku Jamaluddin
creator: Anis Ahmed Khan
creator: Soo Tein Ngoi
creator: Yee Qing Lee
creator: Min Yi Lau
creator: Shiang Chiet Tan
creator: Zhi Xian Kong
creator: Jia Jie Woon
creator: Siew Thong Mak
creator: Kartini Abdul Jabar
creator: Rina Karunakaran
creator: Zalina Ismail
creator: Sharifah Azura Salleh
creator: Siti Suraiya Md Noor
creator: Siti Norbaya Masri
creator: Niazlin Mohd Taib
creator: Azmiza Syawani Jasni
creator: Loong Hua Tee
creator: Kin Chong Leong
creator: Victor Kok Eow Lim
creator: Sazaly Abu Bakar
creator: Cindy Shuan Ju Teh
uri: https://doi.org/10.7717/peerj.16393
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2023 Yap et al.

title: Intraspecific body size variation and allometry of genitalia in the orb-web spider—Argiope lobata
link: https://peerj.com/articles/16413
last-modified: 2023-11-28
description: The current consensus is that sexual selection is responsible for the rapid and diverse evolution of genitalia, with several mutually exclusive mechanisms under debate, including non-antagonistic, antagonistic and stabilizing mechanisms. We used the orb-web spider, Argiope lobata (Araneidae), as a study model to quantify the allometric relationship between body size and genitalia, and to test for any impact of genital structures on male mating success or outcome in terms of copulation duration, leg loss or cannibalism. Our data do not support the ‘one-size-fits-all’ hypothesis that predicts a negative allometric slope between genitalia and body size. Importantly, we measured both male and female genitalia, and there was no sex specific pattern in allometric slopes. Unexpectedly, we found no predictor for reproductive success as indicated by copulation duration, cannibalism, and leg loss.
creator: Chathuranga Dharmarathne
creator: Donald James McLean
creator: Marie E. Herberstein
creator: Jutta M. Schneider
uri: https://doi.org/10.7717/peerj.16413
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2023 Dharmarathne et al.

title: Long-range RNA structures in the human transcriptome beyond evolutionarily conserved regions
link: https://peerj.com/articles/16414
last-modified: 2023-11-28
description: RNA structure has been increasingly recognized as a critical player in the biogenesis and turnover of many transcripts classes. In eukaryotes, the prediction of RNA structure by thermodynamic modeling meets fundamental limitations due to the large sizes and complex, discontinuous organization of eukaryotic genes. Signatures of functional RNA structures can be found by detecting compensatory substitutions in homologous sequences, but a comparative approach is applicable only within conserved sequence blocks. Here, we developed a computational pipeline called PHRIC, which is not limited to conserved regions and relies on RNA contacts derived from RNA in situ conformation sequencing (RIC-seq) experiments. It extracts pairs of short RNA fragments surrounded by nested clusters of RNA contacts and predicts long, nearly perfect complementary base pairings formed between these fragments. In application to a panel of RIC-seq experiments in seven human cell lines, PHRIC predicted ~12,000 stable long-range RNA structures with equilibrium free energy below −15 kcal/mol, the vast majority of which fall outside of regions annotated as conserved among vertebrates. These structures, nevertheless, show some level of sequence conservation and remarkable compensatory substitution patterns in other clades. Furthermore, we found that introns have a higher propensity to form stable long-range RNA structures between each other, and moreover that RNA structures tend to concentrate within the same intron rather than connect adjacent introns. These results for the first time extend the application of proximity ligation assays to RNA structure prediction beyond conserved regions.
creator: Sergey Margasyuk
creator: Lev Zavileyskiy
creator: Changchang Cao
creator: Dmitri Pervouchine
uri: https://doi.org/10.7717/peerj.16414
license: https://creativecommons.org/licenses/by-nc/4.0
rights: © 2023 Margasyuk et al.

title: Lymphoid-specific helicase inhibits cervical cancer cells ferroptosis by promoting Nrf2 expression
link: https://peerj.com/articles/16451
last-modified: 2023-11-28
description: BackgroundCervical cancer is a major cause of morbidity and mortality in women worldwide. The underlying mechanisms of its progression are not well understood. In this study, we investigated the role of lymphoid-specific helicase (HELLS) in cervical cancer.MethodsWe measured HELLS expression in cervical cancer and assessed its function using gain- and loss-of-function experiments. Cell viability was measured using the Cell Counting Kit-8 (CCK8 ) assay, and cell proliferation was analyzed using colony formation and EdU assays.ResultsWe found that HELLS was significantly increased in cervical cancer and that its overexpression promoted cell viability (P < 0.01) and colony formation (P < 0.001). In contrast, si-HELLS suppressed these effects. Moreover, HELLS overexpression inhibited cell death induced by the ferroptosis inducer erastin (P < 0.01). Mechanistically, we found that HELLS promoted cervical cancer proliferation by regulating nuclear factor erythroid 2-related factor 2 (Nrf2)-mediated ferroptosis.ConclusionOur data suggest that HELLS promotes cervical cancer proliferation by inhibiting Nrf2 expression. Therefore, HELLS knockdown may be an effective treatment for cervical cancer.
creator: Weiwei Tie
creator: Fenfen Ge
uri: https://doi.org/10.7717/peerj.16451
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2023 Tie and Ge