Reeling them in: taxonomy of marine annelids used as bait by anglers in the Western Cape Province, South Africa
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 study do not match those from specimens in China and India, respectively. Further research is required to resolve the species complexes detected and also to refine the use of names by fishermen over a wider geographic range.
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
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
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.
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
Where is my arm? Investigating the link between complex regional pain syndrome and poor localisation of the affected limb
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.
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
Association between C-Maf-inducing protein gene rs2287112 polymorphism and schizophrenia
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.
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
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
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.
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
A possible brachiosaurid (Dinosauria, Sauropoda) from the mid-Cretaceous of northeastern China
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.
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
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
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.
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
Exploration of Zoo felids in North-East China for the prevalence and molecular identification of Cryptosporidium spp.
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.
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
Assessment of metrics in next-generation sequencing experiments for use in core-genome multilocus sequence type
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.
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
Inhibition of Kelch-like epichlorohydrin-related protein 1 promotes the progression and drug resistance of lung adenocarcinoma
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 to guide the staging and treatment of lung cancer.
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