PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Reeling them in: taxonomy of marine annelids used as bait by anglers in the Western Cape Province, South Africa
items: Association of serum fetuin-B with insulin resistance and pre-diabetes in young Chinese women: evidence from a cross-sectional study and effect of liraglutide
items: Where is my arm? Investigating the link between complex regional pain syndrome and poor localisation of the affected limb
items: Association between C-Maf-inducing protein gene rs2287112 polymorphism and schizophrenia
items: Phylogeography of high Andean killifishes Orestias (Teleostei: Cyprinodontidae) in Caquena and Lauca sub-basins of the Altiplano (Chile): mitochondrial and nuclear analysis of an endangered fish
items: A possible brachiosaurid (Dinosauria, Sauropoda) from the mid-Cretaceous of northeastern China
items: Inflammatory gene expression profiling in peripheral blood from patients with Alzheimer’s disease reveals key pathways and hub genes with potential diagnostic utility: a preliminary study
items: Exploration of Zoo felids in North-East China for the prevalence and molecular identification of Cryptosporidium spp.
items: Assessment of metrics in next-generation sequencing experiments for use in core-genome multilocus sequence type
items: Inhibition of Kelch-like epichlorohydrin-related protein 1 promotes the progression and drug resistance of lung adenocarcinoma

Reeling them in: taxonomy of marine annelids used as bait by anglers in the Western Cape Province, South Africa
type: item
type: AcademicArticle
description: Background Common names are frequently used inconsistently for marine annelid species used as bait in the peer-reviewed literature, field guides and legislative material. The taxonomy of many such species based on morphology only also ignores cryptic divergences not yet detected. Such inconsistencies hamper effective management of marine annelids, especially as fishing for recreation and subsistence is increasing. This study investigates the scale of the problem by studying the use and names of bait marine annelids in the Western Cape Province of South Africa. Methods Fifteen recreational and six subsistence fishers at 12 popular fishing sites in the Western Cape Province donated 194 worms which they identified by common name. Worms were assigned scientific names according to a standard identification key for polychaetes from South Africa, and mitochondrial cytochrome oxidase I (COI) amplified and sequenced. Results This study identified 11 nominal species known by 10 common names, in the families Siphonosomatidae, Arenicolidae, Sabellaridae, Lumbrineridae, Eunicidae, Onuphidae and Nereididae. Cryptic diversity was investigated through employing mitochondrial COI sequences and these data will facilitate future identifications among widely distributed species. Several species (Siphonosoma dayi, Abarenicola gilchristi, Scoletoma species, Marphysa corallina, Lysidice natalensis, Heptaceras quinquedens, Perinereis latipalpa) are reported as bait for the first time, and while the names blood- and moonshineworms were consistently applied to members of Arenicolidae and Onuphidae, respectively, coralworm was applied to members of Sabellaridae and Nereididae. Analysis of COI sequences supported morphological investigations that revealed the presence of two taxonomic units each for specimens initially identified as Gunnarea gaimardi and Scoletoma tetraura according to identification keys. Similarly, sequences for Scoletoma species and Lysidice natalensis generated in this stu…
format: application/pdf
format: text/html
creator: Carol Simon
creator: Jyothi Kara
creator: Alheit du Toit
creator: Hendré van Rensburg
creator: Caveshlin Naidoo
creator: Conrad A. Matthee
subject: Aquaculture, Fisheries and Fish Science
subject: Biodiversity
subject: Marine Biology
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.11847
publisher: PeerJ Inc.
rights: © 2021 Simon et al.
abstract: Background Common names are frequently used inconsistently for marine annelid species used as bait in the peer-reviewed literature, field guides and legislative material. The taxonomy of many such species based on morphology only also ignores cryptic divergences not yet detected. Such inconsistencies hamper effective management of marine annelids, especially as fishing for recreation and subsistence is increasing. This study investigates the scale of the problem by studying the use and names of bait marine annelids in the Western Cape Province of South Africa. Methods Fifteen recreational and six subsistence fishers at 12 popular fishing sites in the Western Cape Province donated 194 worms which they identified by common name. Worms were assigned scientific names according to a standard identification key for polychaetes from South Africa, and mitochondrial cytochrome oxidase I (COI) amplified and sequenced. Results This study identified 11 nominal species known by 10 common names, in the families Siphonosomatidae, Arenicolidae, Sabellaridae, Lumbrineridae, Eunicidae, Onuphidae and Nereididae. Cryptic diversity was investigated through employing mitochondrial COI sequences and these data will facilitate future identifications among widely distributed species. Several species (Siphonosoma dayi, Abarenicola gilchristi, Scoletoma species, Marphysa corallina, Lysidice natalensis, Heptaceras quinquedens, Perinereis latipalpa) are reported as bait for the first time, and while the names blood- and moonshineworms were consistently applied to members of Arenicolidae and Onuphidae, respectively, coralworm was applied to members of Sabellaridae and Nereididae. Analysis of COI sequences supported morphological investigations that revealed the presence of two taxonomic units each for specimens initially identified as Gunnarea gaimardi and Scoletoma tetraura according to identification keys. Similarly, sequences for Scoletoma species and Lysidice natalensis generated in this stu…
bibliographic citation: Simon et al. (2021) Reeling them in: taxonomy of marine annelids used as bait by anglers in the Western Cape Province, South Africa. PeerJ 9:e11847 https://doi.org/10.7717/peerj.11847
date submitted: 2021-04-09
date accepted: 2021-07-01
issued: 2021-08-20
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Simon
  given name: Carol
author list: Agent
  family name: Kara
  given name: Jyothi
author list: Agent
  family name: du Toit
  given name: Alheit
author list: Agent
  family name: van Rensburg
  given name: Hendré
author list: Agent
  family name: Naidoo
  given name: Caveshlin
author list: Agent
  family name: Matthee
  given name: Conrad A.
doi: 10.7717/peerj.11847
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-08-20
copyright: © 2021 Simon et al.
attribution name: Simon et al.

Association of serum fetuin-B with insulin resistance and pre-diabetes in young Chinese women: evidence from a cross-sectional study and effect of liraglutide
type: item
type: AcademicArticle
description: Background and Aims Fetuin-B has been reported to be involved in glucose and lipid metabolism and associated with the occurrence of diabetes. The main purpose of this study is to explore the changes of circulating fetuin-B in young women with pre-diabetes and to analyze the relationship between fetuin-B and the occurrence and development of IR. Methods A total of 304 women were enrolled in this study and subjected to both OGTT and EHC. A subgroup of 26 overweight/obese womenwas treated with Lira for 24 weeks. serum fetuin-B concentrations were measured by ELISA. Results In IGT and IR-NG groups, serum fetuin-B levels were higher than those in the NGT group. The serum fetuin-B levels in the IGT group were higher than those in the IR-NG group. serum fetuin-B was positively correlated with BMI, WHR, 2h-BG, FIns, HbA1c, and HOMA2-IR, but negatively correlated with the M-value in all study populations. Multiple stepwise regression analysis showed that the M-value was independently and inversely associated with serum fetuin-B. Logistic regression analysis showed that serum fetuin-B was independently associated with IGT and significantly increased the risk of IGT. During the OGTT, serum fetuin-B increased significantly in the NGT group, but there were no significant changes in other groups. During the EHC, serum fetuin-B increased in the IGT group, but there was no change in other groups. After Lira intervention, serum fetuin-B decreased significantly in IGT women. Conclusions serum fetuin-B levels are elevated in young women with IR or IGT and may be associated with IR.
format: application/pdf
format: text/html
creator: Xuyun Xia
creator: Shiyao Xue
creator: Gangyi Yang
creator: Yu Li
creator: Hua Liu
creator: Chen Chen
creator: Ling Li
subject: Clinical Trials
subject: Diabetes and Endocrinology
subject: Internal Medicine
subject: Women’s Health
subject: Metabolic Sciences
description: doi:10.7717/peerj.11869
publisher: PeerJ Inc.
rights: © 2021 Xia et al.
abstract: Background and Aims Fetuin-B has been reported to be involved in glucose and lipid metabolism and associated with the occurrence of diabetes. The main purpose of this study is to explore the changes of circulating fetuin-B in young women with pre-diabetes and to analyze the relationship between fetuin-B and the occurrence and development of IR. Methods A total of 304 women were enrolled in this study and subjected to both OGTT and EHC. A subgroup of 26 overweight/obese womenwas treated with Lira for 24 weeks. serum fetuin-B concentrations were measured by ELISA. Results In IGT and IR-NG groups, serum fetuin-B levels were higher than those in the NGT group. The serum fetuin-B levels in the IGT group were higher than those in the IR-NG group. serum fetuin-B was positively correlated with BMI, WHR, 2h-BG, FIns, HbA1c, and HOMA2-IR, but negatively correlated with the M-value in all study populations. Multiple stepwise regression analysis showed that the M-value was independently and inversely associated with serum fetuin-B. Logistic regression analysis showed that serum fetuin-B was independently associated with IGT and significantly increased the risk of IGT. During the OGTT, serum fetuin-B increased significantly in the NGT group, but there were no significant changes in other groups. During the EHC, serum fetuin-B increased in the IGT group, but there was no change in other groups. After Lira intervention, serum fetuin-B decreased significantly in IGT women. Conclusions serum fetuin-B levels are elevated in young women with IR or IGT and may be associated with IR.
bibliographic citation: Xia et al. (2021) Association of serum fetuin-B with insulin resistance and pre-diabetes in young Chinese women: evidence from a cross-sectional study and effect of liraglutide. PeerJ 9:e11869 https://doi.org/10.7717/peerj.11869
date submitted: 2020-12-26
date accepted: 2021-07-05
issued: 2021-08-20
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Xia
  given name: Xuyun
author list: Agent
  family name: Xue
  given name: Shiyao
author list: Agent
  family name: Yang
  given name: Gangyi
author list: Agent
  family name: Li
  given name: Yu
author list: Agent
  family name: Liu
  given name: Hua
author list: Agent
  family name: Chen
  given name: Chen
author list: Agent
  family name: Li
  given name: Ling
doi: 10.7717/peerj.11869
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-08-20
copyright: ©2021 Xia et al.
attribution name: Xia et al.

Where is my arm? Investigating the link between complex regional pain syndrome and poor localisation of the affected limb
type: item
type: AcademicArticle
description: Background Anecdotally, people living with Complex Regional Pain Syndrome (CRPS) often report difficulties in localising their own affected limb when it is out of view. Experimental attempts to investigate this report have used explicit tasks and yielded varied results. Methods Here we used a limb localisation task that interrogates implicit mechanisms because we first induce a compelling illusion called the Disappearing Hand Trick (DHT). In the DHT, participants judge their hands to be close together when, in fact, they are far apart. Sixteen volunteers with unilateral upper limb CRPS (mean age 39 ± 12 years, four males), 15 volunteers with non-CRPS persistent hand pain (‘pain controls’; mean age 58 ± 13 years, two males) and 29 pain-free volunteers (‘pain-free controls’; mean age 36 ± 19 years, 10 males) performed a hand-localisation task after each of three conditions: the DHT illusion and two control conditions in which no illusion was performed. The conditions were repeated twice (one for each hand). We hypothesised that (1) participants with CRPS would perform worse at hand self-localisation than both the control samples; (2) participants with non-CRPS persistent hand pain would perform worse than pain-free controls; (3) participants in both persistent pain groups would perform worse with their affected hand than with their unaffected hand. Results Our first two hypotheses were not supported. Our third hypothesis was supported —when visually and proprioceptively encoded positions of the hands were incongruent (i.e. after the DHT), relocalisation performance was worse with the affected hand than it was with the unaffected hand. The similar results in hand localisation in the control and pain groups might suggest that, when implicit processes are required, people with CRPS’ ability to localise their limb is preserved.
format: application/pdf
format: text/html
creator: Valeria Bellan
creator: Felicity A. Braithwaite
creator: Erica M. Wilkinson
creator: Tasha R. Stanton
creator: G. Lorimer Moseley
subject: Anesthesiology and Pain Management
subject: Evidence Based Medicine
subject: Global Health
subject: Psychiatry and Psychology
description: doi:10.7717/peerj.11882
publisher: PeerJ Inc.
rights: © 2021 Bellan et al.
abstract: Background Anecdotally, people living with Complex Regional Pain Syndrome (CRPS) often report difficulties in localising their own affected limb when it is out of view. Experimental attempts to investigate this report have used explicit tasks and yielded varied results. Methods Here we used a limb localisation task that interrogates implicit mechanisms because we first induce a compelling illusion called the Disappearing Hand Trick (DHT). In the DHT, participants judge their hands to be close together when, in fact, they are far apart. Sixteen volunteers with unilateral upper limb CRPS (mean age 39 ± 12 years, four males), 15 volunteers with non-CRPS persistent hand pain (‘pain controls’; mean age 58 ± 13 years, two males) and 29 pain-free volunteers (‘pain-free controls’; mean age 36 ± 19 years, 10 males) performed a hand-localisation task after each of three conditions: the DHT illusion and two control conditions in which no illusion was performed. The conditions were repeated twice (one for each hand). We hypothesised that (1) participants with CRPS would perform worse at hand self-localisation than both the control samples; (2) participants with non-CRPS persistent hand pain would perform worse than pain-free controls; (3) participants in both persistent pain groups would perform worse with their affected hand than with their unaffected hand. Results Our first two hypotheses were not supported. Our third hypothesis was supported —when visually and proprioceptively encoded positions of the hands were incongruent (i.e. after the DHT), relocalisation performance was worse with the affected hand than it was with the unaffected hand. The similar results in hand localisation in the control and pain groups might suggest that, when implicit processes are required, people with CRPS’ ability to localise their limb is preserved.
bibliographic citation: Bellan et al. (2021) Where is my arm? Investigating the link between complex regional pain syndrome and poor localisation of the affected limb. PeerJ 9:e11882 https://doi.org/10.7717/peerj.11882
date submitted: 2020-11-26
date accepted: 2021-07-08
issued: 2021-08-20
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Bellan
  given name: Valeria
author list: Agent
  family name: Braithwaite
  given name: Felicity A.
author list: Agent
  family name: Wilkinson
  given name: Erica M.
author list: Agent
  family name: Stanton
  given name: Tasha R.
author list: Agent
  family name: Moseley
  given name: G. Lorimer
doi: 10.7717/peerj.11882
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-08-20
copyright: © 2021 Bellan et al.
attribution name: Bellan et al.

Association between C-Maf-inducing protein gene rs2287112 polymorphism and schizophrenia
type: item
type: AcademicArticle
description: Background Schizophrenia is a severely multifactorial neuropsychiatric disorder, and the majority of cases are due to genetic variations. In this study, we evaluated the genetic association between the C-Maf-inducing protein (CMIP) gene and schizophrenia in the Han Chinese population. Methods In this case-control study, 761 schizophrenia patients and 775 healthy controls were recruited. Tag single-nucleotide polymorphisms (SNPs; rs12925980, rs2287112, rs3751859 and rs77700579) from the CMIP gene were genotyped via matrix-assisted laser desorption/ionization time of flight mass spectrometry. We used logistic regression to estimate the associations between the genotypes/alleles of each SNP and schizophrenia in males and females, respectively. The in-depth link between CMIP and schizophrenia was explored through linkage disequilibrium (LD) and further haplotype analyses. False discovery rate correction was utilized to control for Type I errors caused by multiple comparisons. Results There was a significant difference in rs287112 allele frequencies between female schizophrenia patients and healthy controls after adjusting for multiple comparisons (χ2 = 12.296, Padj = 0.008). Females carrying minor allele G had 4.445 times higher risk of schizophrenia compared with people who carried the T allele (OR = 4.445, 95% CI [1.788–11.046]). Linkage-disequilibrium was not observed in the subjects, and people with haplotype TTGT of rs12925980–rs2287112–rs3751859–rs77700579 had a lower risk of schizophrenia (OR = 0.42, 95% CI [0.19–0.94]) when compared with CTGA haplotypes. However, the association did not survive false discovery rate correction. Conclusion This study identified a potential CMIP variant that may confer schizophrenia risk in the female Han Chinese population.
format: application/pdf
format: text/html
creator: Yingli Fu
creator: Xiaojun Ren
creator: Wei Bai
creator: Qiong Yu
creator: Yaoyao Sun
creator: Yaqin Yu
creator: Na Zhou
subject: Cognitive Disorders
subject: Epidemiology
subject: Public Health
subject: Women’s Health
subject: Medical Genetics
description: doi:10.7717/peerj.11907
publisher: PeerJ Inc.
rights: © 2021 Fu et al.
abstract: Background Schizophrenia is a severely multifactorial neuropsychiatric disorder, and the majority of cases are due to genetic variations. In this study, we evaluated the genetic association between the C-Maf-inducing protein (CMIP) gene and schizophrenia in the Han Chinese population. Methods In this case-control study, 761 schizophrenia patients and 775 healthy controls were recruited. Tag single-nucleotide polymorphisms (SNPs; rs12925980, rs2287112, rs3751859 and rs77700579) from the CMIP gene were genotyped via matrix-assisted laser desorption/ionization time of flight mass spectrometry. We used logistic regression to estimate the associations between the genotypes/alleles of each SNP and schizophrenia in males and females, respectively. The in-depth link between CMIP and schizophrenia was explored through linkage disequilibrium (LD) and further haplotype analyses. False discovery rate correction was utilized to control for Type I errors caused by multiple comparisons. Results There was a significant difference in rs287112 allele frequencies between female schizophrenia patients and healthy controls after adjusting for multiple comparisons (χ2 = 12.296, Padj = 0.008). Females carrying minor allele G had 4.445 times higher risk of schizophrenia compared with people who carried the T allele (OR = 4.445, 95% CI [1.788–11.046]). Linkage-disequilibrium was not observed in the subjects, and people with haplotype TTGT of rs12925980–rs2287112–rs3751859–rs77700579 had a lower risk of schizophrenia (OR = 0.42, 95% CI [0.19–0.94]) when compared with CTGA haplotypes. However, the association did not survive false discovery rate correction. Conclusion This study identified a potential CMIP variant that may confer schizophrenia risk in the female Han Chinese population.
bibliographic citation: Fu et al. (2021) Association between C-Maf-inducing protein gene rs2287112 polymorphism and schizophrenia. PeerJ 9:e11907 https://doi.org/10.7717/peerj.11907
date submitted: 2021-02-22
date accepted: 2021-07-14
issued: 2021-08-20
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Fu
  given name: Yingli
author list: Agent
  family name: Ren
  given name: Xiaojun
author list: Agent
  family name: Bai
  given name: Wei
author list: Agent
  family name: Yu
  given name: Qiong
author list: Agent
  family name: Sun
  given name: Yaoyao
author list: Agent
  family name: Yu
  given name: Yaqin
author list: Agent
  family name: Zhou
  given name: Na
doi: 10.7717/peerj.11907
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-08-20
copyright: © 2021 Fu et al.
attribution name: Fu et al.

Phylogeography of high Andean killifishes Orestias (Teleostei: Cyprinodontidae) in Caquena and Lauca sub-basins of the Altiplano (Chile): mitochondrial and nuclear analysis of an endangered fish
type: item
type: AcademicArticle
description: From the early Miocene, the uplift of the Andes Mountains, intense volcanic activity and the occurrence of successive periods of dryness and humidity would have differentially influenced the modification of Altiplano watersheds, and consequently the evolutionary history of the taxa that live there. We analyzed Orestias populations from the Caquena and Lauca Altiplanic sub-basins of northern Chile to determine their genetic differentiation and relationship to their geographical distribution using mitochondrial (D-loop) and nuclear (microsatellite) molecular markers and to reconstruct its biogeographic history on these sub-basins. The results allowed reconstructing and reevaluating the evolutionary history of the genus in the area; genic diversity and differentiation together with different founding genetic groups suggest that Orestias have been spread homogeneously in the study area and would have experienced local disturbances that promoted isolation and diversification in restricted zones of their distribution.
format: application/pdf
format: text/html
creator: Violeta Cárcamo-Tejer
creator: Irma Vila
creator: Francisco Llanquín-Rosas
creator: Alberto Sáez-Arteaga
creator: Claudia Guerrero-Jiménez
subject: Biogeography
subject: Genetics
subject: Molecular Biology
subject: Zoology
subject: Freshwater Biology
description: doi:10.7717/peerj.11917
publisher: PeerJ Inc.
rights: © 2021 Cárcamo-Tejer et al.
abstract: From the early Miocene, the uplift of the Andes Mountains, intense volcanic activity and the occurrence of successive periods of dryness and humidity would have differentially influenced the modification of Altiplano watersheds, and consequently the evolutionary history of the taxa that live there. We analyzed Orestias populations from the Caquena and Lauca Altiplanic sub-basins of northern Chile to determine their genetic differentiation and relationship to their geographical distribution using mitochondrial (D-loop) and nuclear (microsatellite) molecular markers and to reconstruct its biogeographic history on these sub-basins. The results allowed reconstructing and reevaluating the evolutionary history of the genus in the area; genic diversity and differentiation together with different founding genetic groups suggest that Orestias have been spread homogeneously in the study area and would have experienced local disturbances that promoted isolation and diversification in restricted zones of their distribution.
bibliographic citation: Cárcamo-Tejer et al. (2021) Phylogeography of high Andean killifishes Orestias (Teleostei: Cyprinodontidae) in Caquena and Lauca sub-basins of the Altiplano (Chile): mitochondrial and nuclear analysis of an endangered fish. PeerJ 9:e11917 https://doi.org/10.7717/peerj.11917
date submitted: 2020-10-30
date accepted: 2021-07-15
issued: 2021-08-20
is part of: PeerJ
license: https://creativeco\relax \special {t4ht= }mMons.org/licenses/by/4.0/
author list: Agent
  family name: Cárcamo-Tejer
  given name: Violeta
author list: Agent
  family name: Vila
  given name: Irma
author list: Agent
  family name: Llanquín-Rosas
  given name: Francisco
author list: Agent
  family name: Sáez-Arteaga
  given name: Alberto
author list: Agent
  family name: Guerrero-Jiménez
  given name: Claudia
doi: 10.7717/peerj.11917
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-08-20
copyright: ©2021 Cárcamo-Tejer et al.
attribution name: Cárcamo-Tejer et al.

A possible brachiosaurid (Dinosauria, Sauropoda) from the mid-Cretaceous of northeastern China
type: item
type: AcademicArticle
description: Brachiosauridae is a lineage of titanosauriform sauropods that includes some of the most iconic non-avian dinosaurs. Undisputed brachiosaurid fossils are known from the Late Jurassic through the Early Cretaceous of North America, Africa, and Europe, but proposed occurrences outside this range have proven controversial. Despite occasional suggestions that brachiosaurids dispersed into Asia, to date no fossils have provided convincing evidence for a pan-Laurasian distribution for the clade, and the failure to discover brachiosaurid fossils in the well-sampled sauropod-bearing horizons of the Early Cretaceous of Asia has been taken to evidence their genuine absence from the continent. Here we report on an isolated sauropod maxilla from the middle Cretaceous (Albian–Cenomanian) Longjing Formation of the Yanji basin of northeast China. Although the specimen preserves limited morphological information, it exhibits axially twisted dentition, a shared derived trait otherwise known only in brachiosaurids. Referral of the specimen to the Brachiosauridae receives support from phylogenetic analysis under both equal and implied weights parsimony, providing the most convincing evidence to date that brachiosaurids dispersed into Asia at some point in their evolutionary history. Inclusion in our phylogenetic analyses of an isolated sauropod dentary from the same site, for which an association with the maxilla is possible but uncertain, does not substantively alter these results. We consider several paleobiogeographic scenarios that could account for the occurrence of a middle Cretaceous Asian brachiosaurid, including dispersal from either North America or Europe during the Early Cretaceous. The identification of a brachiosaurid in the Longshan fauna, and the paleobiogeographic histories that could account for its presence there, are hypotheses that can be tested with continued study and excavation of fossils from the Longjing Formation.
format: application/pdf
format: text/html
creator: Chun-Chi Liao
creator: Andrew Moore
creator: Changzhu Jin
creator: Tzu-Ruei Yang
creator: Masateru Shibata
creator: Feng Jin
creator: Bing Wang
creator: Dongchun Jin
creator: Yu Guo
creator: Xing Xu
subject: Evolutionary Studies
subject: Paleontology
subject: Zoology
description: doi:10.7717/peerj.11957
publisher: PeerJ Inc.
rights: © 2021 Liao et al.
abstract: Brachiosauridae is a lineage of titanosauriform sauropods that includes some of the most iconic non-avian dinosaurs. Undisputed brachiosaurid fossils are known from the Late Jurassic through the Early Cretaceous of North America, Africa, and Europe, but proposed occurrences outside this range have proven controversial. Despite occasional suggestions that brachiosaurids dispersed into Asia, to date no fossils have provided convincing evidence for a pan-Laurasian distribution for the clade, and the failure to discover brachiosaurid fossils in the well-sampled sauropod-bearing horizons of the Early Cretaceous of Asia has been taken to evidence their genuine absence from the continent. Here we report on an isolated sauropod maxilla from the middle Cretaceous (Albian–Cenomanian) Longjing Formation of the Yanji basin of northeast China. Although the specimen preserves limited morphological information, it exhibits axially twisted dentition, a shared derived trait otherwise known only in brachiosaurids. Referral of the specimen to the Brachiosauridae receives support from phylogenetic analysis under both equal and implied weights parsimony, providing the most convincing evidence to date that brachiosaurids dispersed into Asia at some point in their evolutionary history. Inclusion in our phylogenetic analyses of an isolated sauropod dentary from the same site, for which an association with the maxilla is possible but uncertain, does not substantively alter these results. We consider several paleobiogeographic scenarios that could account for the occurrence of a middle Cretaceous Asian brachiosaurid, including dispersal from either North America or Europe during the Early Cretaceous. The identification of a brachiosaurid in the Longshan fauna, and the paleobiogeographic histories that could account for its presence there, are hypotheses that can be tested with continued study and excavation of fossils from the Longjing Formation.
bibliographic citation: Liao et al. (2021) A possible brachiosaurid (Dinosauria, Sauropoda) from the mid-Cretaceous of northeastern China. PeerJ 9:e11957 https://doi.org/10.7717/peerj.11957
date submitted: 2021-05-14
date accepted: 2021-07-21
issued: 2021-08-20
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Liao
  given name: Chun-Chi
author list: Agent
  family name: Moore
  given name: Andrew
author list: Agent
  family name: Jin
  given name: Changzhu
author list: Agent
  family name: Yang
  given name: Tzu-Ruei
author list: Agent
  family name: Shibata
  given name: Masateru
author list: Agent
  family name: Jin
  given name: Feng
author list: Agent
  family name: Wang
  given name: Bing
author list: Agent
  family name: Jin
  given name: Dongchun
author list: Agent
  family name: Guo
  given name: Yu
author list: Agent
  family name: Xu
  given name: Xing
doi: 10.7717/peerj.11957
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-08-20
copyright: © 2021 Liao et al.
attribution name: Liao et al.

Inflammatory gene expression profiling in peripheral blood from patients with Alzheimer’s disease reveals key pathways and hub genes with potential diagnostic utility: a preliminary study
type: item
type: AcademicArticle
description: Background Alzheimer’s disease (AD) is an age-related neurodegenerative disease caused by central nervous system disorders. Late-onset Alzheimer disease (LOAD) is the most common neurodegenerative disorder worldwide. Differences at the expression level of certain genes, resulting from either genetic variations or environmental interactions, might be one of the mechanisms underlying differential risks for developing AD. Peripheral blood genome transcriptional profiling may provide a powerful and minimally invasive tool for the identification of novel targets beyond Aβ and tau for AD research. Methods This preliminary study explores molecular pathogenesis of LOAD-related inflammation through next generation sequencing, to assess RNA expression profiles in peripheral blood from five patients with LOAD and 10 healthy controls. Results The analysis of RNA expression profiles revealed 94 genes up-regulated and 147 down-regulated. Gene function analysis, including Gene Ontology (GO) and KOBAS-Kyoto Encyclopedia of DEGs and Genomes (KEGG) pathways indicated upregulation of interferon family (INF) signaling, while the down-regulated genes were mainly associated with the cell cycle process. KEGG metabolic pathways mapping showed gene expression alterations in the signaling pathways of JAK/STAT, chemokines, MAP kinases and Alzheimer disease. The results of this preliminary study provided not only a comprehensive picture of gene expression, but also the key processes associated with pathology for the regulation of neuroinflammation, to improve the current mechanisms to treat LOAD.
format: application/pdf
format: text/html
creator: Kelly Cardona
creator: Javier Medina
creator: Mary Orrego-Cardozo
creator: Francia Restrepo de Mejía
creator: Xabier Elcoroaristizabal
creator: Carlos Andrés Naranjo Galvis
subject: Bioinformatics
subject: Molecular Biology
subject: Cognitive Disorders
subject: Geriatrics
subject: Neurology
description: doi:10.7717/peerj.12016
publisher: PeerJ Inc.
rights: © 2021 Cardona et al.
abstract: Background Alzheimer’s disease (AD) is an age-related neurodegenerative disease caused by central nervous system disorders. Late-onset Alzheimer disease (LOAD) is the most common neurodegenerative disorder worldwide. Differences at the expression level of certain genes, resulting from either genetic variations or environmental interactions, might be one of the mechanisms underlying differential risks for developing AD. Peripheral blood genome transcriptional profiling may provide a powerful and minimally invasive tool for the identification of novel targets beyond Aβ and tau for AD research. Methods This preliminary study explores molecular pathogenesis of LOAD-related inflammation through next generation sequencing, to assess RNA expression profiles in peripheral blood from five patients with LOAD and 10 healthy controls. Results The analysis of RNA expression profiles revealed 94 genes up-regulated and 147 down-regulated. Gene function analysis, including Gene Ontology (GO) and KOBAS-Kyoto Encyclopedia of DEGs and Genomes (KEGG) pathways indicated upregulation of interferon family (INF) signaling, while the down-regulated genes were mainly associated with the cell cycle process. KEGG metabolic pathways mapping showed gene expression alterations in the signaling pathways of JAK/STAT, chemokines, MAP kinases and Alzheimer disease. The results of this preliminary study provided not only a comprehensive picture of gene expression, but also the key processes associated with pathology for the regulation of neuroinflammation, to improve the current mechanisms to treat LOAD.
bibliographic citation: Cardona et al. (2021) Inflammatory gene expression profiling in peripheral blood from patients with Alzheimer’s disease reveals key pathways and hub genes with potential diagnostic utility: a preliminary study. PeerJ 9:e12016 https://doi.org/10.7717/peerj.12016
date submitted: 2021-03-15
date accepted: 2021-07-29
issued: 2021-08-20
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Cardona
  given name: Kelly
author list: Agent
  family name: Medina
  given name: Javier
author list: Agent
  family name: Orrego-Cardozo
  given name: Mary
author list: Agent
  family name: Restrepo de Mejía
  given name: Francia
author list: Agent
  family name: Elcoroaristizabal
  given name: Xabier
author list: Agent
  family name: Naranjo Galvis
  given name: Carlos Andrés
doi: 10.7717/peerj.12016
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-08-20
copyright: ©2021 Cardona et al.
attribution name: Cardona et al.

Exploration of Zoo felids in North-East China for the prevalence and molecular identification of Cryptosporidium spp.
type: item
type: AcademicArticle
description: Cryptosporidium spp. is a protozoan having the potential to cause zoonosis in humans and animals. Despite the zoonotic importance of this protozoan parasite, limited data are available about its prevalence in zoo felids in North-Eastern China. Hence, the current study was designed to determine the occurrence and molecular characterization of Cryptosporidium spp. from the fecal samples of captive zoo felids. Fecal samples (N = 244) were collected from different felids from five different zoos of North-Eastern China. 18S rRNA gene was amplified from the genomic DNA using species specific primers in nested polymerase chain reaction (nPCR) and Cryptosporidium parvum and Cryptosporidium spp. was found. The overall prevalence of Cryptosporidium was 9.43% (23/244). The 18S rRNA gene similarity analysis showed that 6 Cryptosporidium isolates were Cryptosporidium parvum and the remaining 17 Cryptosporidium isolates were resembling to a Cryptosporidium spp., which is similar to Cryptosporidium NEV10. Phylogenetic tree was constructed based on 18S rRNA of Cryptosporidium spp. The similarity of Cryptosporidium parvum was with its other isolates in China, India, Iran, Iraq, Turkey, Czech Republic, Spain and USA while Cryptosporidium NEV10 alike had a close relationship with Turkish isolates. In conclusion, Cryptosporidium was prevailing in feline animals of China zoo and zoo officials are directed to consider their control policy as it can be a cause of zoonosis.
format: application/pdf
format: text/html
creator: Shakeel Hussain
creator: Syed Mohsin Bukhari
creator: Lixin Wang
creator: Nimra Khalid
creator: Zhijun Hou
subject: Genomics
subject: Molecular Biology
subject: Veterinary Medicine
subject: Zoology
description: doi:10.7717/peerj.11819
publisher: PeerJ Inc.
rights: © 2021 Hussain et al.
abstract: Cryptosporidium spp. is a protozoan having the potential to cause zoonosis in humans and animals. Despite the zoonotic importance of this protozoan parasite, limited data are available about its prevalence in zoo felids in North-Eastern China. Hence, the current study was designed to determine the occurrence and molecular characterization of Cryptosporidium spp. from the fecal samples of captive zoo felids. Fecal samples (N = 244) were collected from different felids from five different zoos of North-Eastern China. 18S rRNA gene was amplified from the genomic DNA using species specific primers in nested polymerase chain reaction (nPCR) and Cryptosporidium parvum and Cryptosporidium spp. was found. The overall prevalence of Cryptosporidium was 9.43% (23/244). The 18S rRNA gene similarity analysis showed that 6 Cryptosporidium isolates were Cryptosporidium parvum and the remaining 17 Cryptosporidium isolates were resembling to a Cryptosporidium spp., which is similar to Cryptosporidium NEV10. Phylogenetic tree was constructed based on 18S rRNA of Cryptosporidium spp. The similarity of Cryptosporidium parvum was with its other isolates in China, India, Iran, Iraq, Turkey, Czech Republic, Spain and USA while Cryptosporidium NEV10 alike had a close relationship with Turkish isolates. In conclusion, Cryptosporidium was prevailing in feline animals of China zoo and zoo officials are directed to consider their control policy as it can be a cause of zoonosis.
bibliographic citation: Hussain et al. (2021) Exploration of Zoo felids in North-East China for the prevalence and molecular identification of Cryptosporidium spp.. PeerJ 9:e11819 https://doi.org/10.7717/peerj.11819
date submitted: 2020-10-15
date accepted: 2021-06-29
issued: 2021-08-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hussain
  given name: Shakeel
author list: Agent
  family name: Mohsin Bukhari
  given name: Syed
author list: Agent
  family name: Wang
  given name: Lixin
author list: Agent
  family name: Khalid
  given name: Nimra
author list: Agent
  family name: Hou
  given name: Zhijun
doi: 10.7717/peerj.11819
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-08-19
copyright: © 2021 Hussain et al.
attribution name: Hussain et al.

Assessment of metrics in next-generation sequencing experiments for use in core-genome multilocus sequence type
type: item
type: AcademicArticle
description: With the reduction in the cost of next-generation sequencing, whole-genome sequencing (WGS)–based methods such as core-genome multilocus sequence type (cgMLST) have been widely used. However, gene-based methods are required to assemble raw reads to contigs, thus possibly introducing errors into assemblies. Because the robustness of cgMLST depends on the quality of assemblies, the results of WGS should be assessed (from sequencing to assembly). In this study, we investigated the robustness of different read lengths, read depths, and assemblers in recovering genes from reference genomes. Different combinations of read lengths and read depths were simulated from the complete genomes of three common food-borne pathogens: Escherichia coli, Listeria monocytogenes, and Salmonella enterica. We found that the quality of assemblies was mainly affected by read depth, irrespective of the assembler used. In addition, we suggest several cutoff values for future cgMLST experiments. Furthermore, we recommend the combinations of read lengths, read depths, and assemblers that can result in a higher cost/performance ratio for cgMLST.
format: application/pdf
format: text/html
creator: Yen-Yi Liu
creator: Bo-Han Chen
creator: Chih-Chieh Chen
creator: Chien-Shun Chiou
subject: Bioinformatics
subject: Genomics
subject: Microbiology
description: doi:10.7717/peerj.11842
publisher: PeerJ Inc.
rights: © 2021 Liu et al.
abstract: With the reduction in the cost of next-generation sequencing, whole-genome sequencing (WGS)–based methods such as core-genome multilocus sequence type (cgMLST) have been widely used. However, gene-based methods are required to assemble raw reads to contigs, thus possibly introducing errors into assemblies. Because the robustness of cgMLST depends on the quality of assemblies, the results of WGS should be assessed (from sequencing to assembly). In this study, we investigated the robustness of different read lengths, read depths, and assemblers in recovering genes from reference genomes. Different combinations of read lengths and read depths were simulated from the complete genomes of three common food-borne pathogens: Escherichia coli, Listeria monocytogenes, and Salmonella enterica. We found that the quality of assemblies was mainly affected by read depth, irrespective of the assembler used. In addition, we suggest several cutoff values for future cgMLST experiments. Furthermore, we recommend the combinations of read lengths, read depths, and assemblers that can result in a higher cost/performance ratio for cgMLST.
bibliographic citation: Liu et al. (2021) Assessment of metrics in next-generation sequencing experiments for use in core-genome multilocus sequence type. PeerJ 9:e11842 https://doi.org/10.7717/peerj.11842
date submitted: 2021-04-21
date accepted: 2021-07-01
issued: 2021-08-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Liu
  given name: Yen-Yi
author list: Agent
  family name: Chen
  given name: Bo-Han
author list: Agent
  family name: Chen
  given name: Chih-Chieh
author list: Agent
  family name: Chiou
  given name: Chien-Shun
doi: 10.7717/peerj.11842
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-08-19
copyright: ©2021 Liu et al.
attribution name: Liu et al.

Inhibition of Kelch-like epichlorohydrin-related protein 1 promotes the progression and drug resistance of lung adenocarcinoma
type: item
type: AcademicArticle
description: Background Lung cancer is a common malignant carcinoma of respiratory system with high morbidity and mortality. Kelch-like epichlorohydrin-related protein 1 (Keap1), a member of the BTB-Kelch protein family, has been reported as an important molecule in several cancers. However, its potential role in tumor is still controversial. Here we aim to clarify the effect of Keap1 on the biological characteristics and chemotherapy resistance in lung adenocarcinoma (LUAD). Methods Immunohistochemistry was conducted to compare Keap1 expression in lung adenocarcinoma tissues and matched non-cancerous tissues, and the correlation between Keap1 expression and clinicopathological features was analyzed. Subsequently, the stable A549 and H1299 cell lines with Keap1 knockdown or overexpression were constructed using lentivirus. The roles of Keap1 on the cell proliferation, migration, invasion and drug resistance were investigated by colony formation assay, cell proliferation assay, wound scratch test, transwell invasion assay and drug sensitivity assay, respectively. Results Keap1 was lowly expressed in tumor tissues compared to matched non-cancerous tissues, and its expression was correlated with TNM stage and lymph node metastasis. Early stage (I) tumors without lymph node metastasis had higher levels of Keap1 expression compared with late-stage tumors (II, III) with the presence of lymphatic metastasis. Colony formation assays showed that Keap1 knockdown promoted the proliferation of A549 and H1299 cells, and the cell growth curves further confirmed this feature. In contrast, wound scratch and transwell invasion experiments showed that Keap1 overexpression inhibited cell migration and invasive malignancy. The IC50 for cisplatin and paclitaxel were significantly increased by Keap1 knockdown in A549 and H1299 cell lines. Conclusion Keap1 knockdown promotes tumor cell growth, proliferation, invasion, metastasis and chemotherapy resistance in LUAD. It may be a potential tumor marker t…
format: application/pdf
format: text/html
creator: Hong Gao
creator: Peipei Tang
creator: Kejie Ni
creator: Lun Zhu
creator: Song Chen
creator: Yulong Zheng
creator: Yufeng Wan
subject: Biochemistry
subject: Cell Biology
subject: Molecular Biology
subject: Pathology
subject: Respiratory Medicine
description: doi:10.7717/peerj.11908
publisher: PeerJ Inc.
rights: © 2021 Gao et al.
abstract: Background Lung cancer is a common malignant carcinoma of respiratory system with high morbidity and mortality. Kelch-like epichlorohydrin-related protein 1 (Keap1), a member of the BTB-Kelch protein family, has been reported as an important molecule in several cancers. However, its potential role in tumor is still controversial. Here we aim to clarify the effect of Keap1 on the biological characteristics and chemotherapy resistance in lung adenocarcinoma (LUAD). Methods Immunohistochemistry was conducted to compare Keap1 expression in lung adenocarcinoma tissues and matched non-cancerous tissues, and the correlation between Keap1 expression and clinicopathological features was analyzed. Subsequently, the stable A549 and H1299 cell lines with Keap1 knockdown or overexpression were constructed using lentivirus. The roles of Keap1 on the cell proliferation, migration, invasion and drug resistance were investigated by colony formation assay, cell proliferation assay, wound scratch test, transwell invasion assay and drug sensitivity assay, respectively. Results Keap1 was lowly expressed in tumor tissues compared to matched non-cancerous tissues, and its expression was correlated with TNM stage and lymph node metastasis. Early stage (I) tumors without lymph node metastasis had higher levels of Keap1 expression compared with late-stage tumors (II, III) with the presence of lymphatic metastasis. Colony formation assays showed that Keap1 knockdown promoted the proliferation of A549 and H1299 cells, and the cell growth curves further confirmed this feature. In contrast, wound scratch and transwell invasion experiments showed that Keap1 overexpression inhibited cell migration and invasive malignancy. The IC50 for cisplatin and paclitaxel were significantly increased by Keap1 knockdown in A549 and H1299 cell lines. Conclusion Keap1 knockdown promotes tumor cell growth, proliferation, invasion, metastasis and chemotherapy resistance in LUAD. It may be a potential tumor marker t…
bibliographic citation: Gao et al. (2021) Inhibition of Kelch-like epichlorohydrin-related protein 1 promotes the progression and drug resistance of lung adenocarcinoma. PeerJ 9:e11908 https://doi.org/10.7717/peerj.11908
date submitted: 2021-01-12
date accepted: 2021-07-14
issued: 2021-08-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Gao
  given name: Hong
author list: Agent
  family name: Tang
  given name: Peipei
author list: Agent
  family name: Ni
  given name: Kejie
author list: Agent
  family name: Zhu
  given name: Lun
author list: Agent
  family name: Chen
  given name: Song
author list: Agent
  family name: Zheng
  given name: Yulong
author list: Agent
  family name: Wan
  given name: Yufeng
doi: 10.7717/peerj.11908
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-08-19
copyright: © 2021 Gao et al.
attribution name: Gao et al.

PeerJ
type: Periodical
uri: PeerJ
issn: 2167-8359