Computer vision supports primary access to meat by early Homo 1.84 million years ago
Human carnivory is atypical among primates. Unlike chimpanzees and bonobos, who are known to hunt smaller monkeys and eat them immediately, human foragers often cooperate to kill large animals and transport them to a safe location to be shared. While it is known that meat became an important part of the hominin diet around 2.6–2 Mya, whether intense cooperation and food sharing developed in conjunction with the regular intake of meat remains unresolved. A widespread assumption is that early hominins acquired animal protein through klepto-parasitism at felid kills. This should be testable by detecting felid-specific bone modifications and tooth marks on carcasses consumed by hominins. Here, deep learning (DL) computer vision was used to identify agency through the analysis of tooth pits and scores on bones recovered from the Early Pleistocene site of DS (Bed I, Olduvai Gorge). We present the first objective evidence of primary access to meat by hominins 1.8 Mya by showing that the most common securely detectable bone-modifying fissipeds at the site were hyenas. The absence of felid modifications in most of the carcasses analyzed indicates that hominins were the primary consumers of most animals accumulated at the site, with hyenas intervening at the post-depositional stage. This underscores the role of hominins as a prominent part of the early Pleistocene African carnivore guild. It also stresses the major (and potentially regular) role that meat played in the diet that configured the emergence of early Homo.
Cobo-Sánchez et al. (2022) Computer vision supports primary access to meat by early Homo 1.84 million years ago. PeerJ 10:e14148 https://doi.org/10.7717/peerj.14148
Proteomic analysis of IgM antigens from mammary tissue under pre- and post-cancer conditions using the MMTV-PyVT mouse model
We analyzed the recognition of tumor antigens by IgM in transgenic MMTV-PyVT mice. PyVT female mice are a model of breast cancer that simulates its counterpart in humans. The PyVT model allows studying antigen recognition in two conditions: before and during tumor expression. We attempted to identify by sequence, the antigens recognized by IgM that are expressed or disappear in the membrane of breast transgenic tissue during the transition “No tumor-Tumor”. 2D immunoblots were obtained of isolated membranes from the breast tissue in the fifth, sixth, and seventh week (transition point). Proteins recognized by IgM were sequenced in duplicate by MALDI-TOF. In the transition, we observed the disappearance of antigens in transgenic mice with respect to non-transgenic ones. We believe that in the diagnosis of cancer in its early stages, the expression of early antigens is as important as their early delocalization, with the latter having the advantage that, under normal conditions, we can know which proteins should be present at a given time. Therefore, we could consider that also the absence of antigens could be considered as a biomarker of cancer in progress.
Hernández Ávila et al. (2022) Proteomic analysis of IgM antigens from mammary tissue under pre- and post-cancer conditions using the MMTV-PyVT mouse model. PeerJ 10:e14175 https://doi.org/10.7717/peerj.14175
A retrospective study of prevalence and pattern of international consensus on ANA patterns among patients with hepatitis C virus infection
Background A previous study reported a 30% prevalence of various autoantibodies among patients with hepatitis C virus (HCV) infection. The International Consensus on Anti-Nuclear Antibody (ANA) Patterns was recently introduced to classify ANA patterns based on immunoassay on HEp-2 cells. There is no previous report with this newly developed classification to evaluate patients with HCV infection. The study aims to study the prevalence and pattern of ANA patterns among HCV-infected patients. Methods We retrospectively analyzed the medical records of patients with HCV infection from September 2020 to June 2021 at our institution. A positive ANA is defined as a titer of more than 1:320. We compared patient features among the positive and negative groups. Results Overall, 258 patients were enrolled—184 patients with negative ANA and 74 patients (28.7%) with positive ANA. The mean age was 67.3 in ANA positive group and 61.2 ANA negative group. Female was prominent with ANA positive and accounted for 63.5%. The most detected ANA pattern was AC-1(homogeneous) (25.9%), followed by AC-4(fine speckled) (25.2%) and AC-21(anti-mitochondrial antibody) (9.6%). In ANA positive group, we found a trend of lower HCV viral load (5.72 log10 IU/ML vs. 6.02 log10 IU/ML), lower alanine aminotransferase level (39.5 U/L vs. 44 U/L), and higher advanced fibrosis (F3 and F4) (38.5% vs. 26.1%). In addition, higher positive ANA (more than 1:640) is significantly associated with lower estimated glomerular filtration rate (eGFR) (77.76 vs. 87.94 mL/min/1.73 m2, P = 0.044). Conclusions A high prevalence (28.7%) of ANA was found in patients with chronic hepatitis C. The presence of positive ANA is not related to the severity of their hepatic manifestation. However, higher positive ANA was significantly associated with lower eGFR.
Hsiao et al. (2022) A retrospective study of prevalence and pattern of international consensus on ANA patterns among patients with hepatitis C virus infection. PeerJ 10:e14200 https://doi.org/10.7717/peerj.14200
IQGAP3 in clear cell renal cell carcinoma contributes to drug resistance and genome stability
Background Clear cell renal clear cell carcinoma (ccRCC) is resistant to most chemotherapeutic drugs and the molecular mechanisms have not been fully revealed. Genomic instability and the abnormal activation of bypass DNA repair pathway is the potential cause of tumor resistance to radiotherapy and chemotherapy. IQ-motif GTPase activating protein 3 (IQGAP3) regulates cell migration and intercellular adhesion. This study aims to analysis the effects of IQGAP3 expression on cell survival, genome stability and clinical prognosis in ccRCC. Methods Multiple bioinformatics analysis based on TCGA database and IHC analysis on clinical specimens were included. Quantitative real-time polymerase chain reaction (qRT-PCR) and western blot (WB) were used to determine protein expression level. MTT assay and 3D spheroid cell growth assay were used to assess cell proliferation and drug resistance in RNAi transfected ccRCC cells. Cell invasion capacity was evaluated by transwell assay. The influence of IQGAP3 on genome instability was revealed by micronuclei number and γ H2AX recruitment test. Results The highly expressed IQGAP3 in multiple subtypes of renal cell carcinoma has a clear prognostic value. Deletion of IQGAP3 inhibits cell growth in 3D Matrigel. IQGAP3 depletion lso increases accumulated DNA damage, and improves cell sensitivity to ionizing radiation and chemotherapeutic drugs. Therefore, targeting DNA damage repair function of IQGAP3 in tumorigenesis can provide ideas for the development of new targets for early diagnosis.
Li et al. (2022) IQGAP3 in clear cell renal cell carcinoma contributes to drug resistance and genome stability. PeerJ 10:e14201 https://doi.org/10.7717/peerj.14201
Quantitative real-time PCR analysis of bacterial biomarkers enable fast and accurate monitoring in inflammatory bowel disease
Inflammatory bowel diseases (IBD) affect millions of people worldwide with increasing incidence. Ulcerative colitis (UC) and Crohn’s disease (CD) are the two most common IBDs. There is no definite cure for IBD, and response to treatment greatly vary among patients. Therefore, there is urgent need for biomarkers to monitor therapy efficacy, and disease prognosis. We aimed to test whether qPCR analysis of common candidate bacteria identified from a patient’s individual fecal microbiome can be used as a fast and reliable personalized microbial biomarker for efficient monitoring of disease course in IBD. Next generation sequencing (NGS) of 16S rRNA gene region identified species level microbiota profiles for a subset of UC, CD, and control samples. Common high abundance bacterial species observed in all three groups, and reported to be associated with IBD are chosen as candidate marker species. These species, and total bacteria amount are quantified in all samples with qPCR. Relative abundance of anti-inflammatory, beneficial Faecalibacterium prausnitzii, Akkermansia muciniphila, and Streptococcus thermophilus was significantly lower in IBD compared to control samples. Moreover, the relative abundance of the examined common species was correlated with the severity of IBD disease. The variance in qPCR data was much lower compared to NGS data, and showed much higher statistical power for clinical utility. The qPCR analysis of target common bacterial species can be a powerful, cost and time efficient approach for monitoring disease status and identify better personalized treatment options for IBD patients.
Sezgin et al. (2022) Quantitative real-time PCR analysis of bacterial biomarkers enable fast and accurate monitoring in inflammatory bowel disease. PeerJ 10:e14217 https://doi.org/10.7717/peerj.14217
Comprehensive screening of low nitrogen tolerant maize based on multiple traits at the seedling stage
Background Plants tolerant to low nitrogen are a quantitative trait affected by many factors, and the different parameters were used for stress-tolerant plant screening in different investigations. But there is no agreement on the use of these indicators. Therefore, a method that can integrate different parameters to evaluate stress tolerance is urgently needed. Methods Six maize genotypes were subject to low nitrogen stress for twenty days. Then seventeen traits of the six maize genotypes related to nitrogen were investigated. Nitrogen tolerance coefficient (NTC) was calculated as low nitrogen traits to high nitrogen traits. Then principal component analysis was conducted based on the NTC. Based on fuzzy mathematics theory, a D value (decimal comprehensive evaluation value) was introduced to evaluate maize tolerant to low nitrogen. Results Three maize (SY998, GEMS42-I and GEMS42-II) with the higher D value have better growth and higher nitrogen accumulation under low nitrogen conditions. In contrast, Ji846 with the lowest D value has the lowest nitrogen accumulation and biomass in response to nitrogen limitation. These results indicated that the D value could help to screen low nitrogen tolerant maize, given that the D value was positively correlated with low nitrogen tolerance in maize seedlings. Conclusions The present study introduced the D value to evaluate stress tolerance. The higher the D value, the greater tolerance of maize to low nitrogen stress. This method may reduce the complexity of the investigated traits and enhance the accuracy of stress-tolerant evaluation. In addition, this method not only can screen potentially tolerant germplasm for low-nitrogen tolerance quickly, but also can comprise the correlated traits as many as possible to avoid the one-sidedness of a single parameter.
Miao et al. (2022) Comprehensive screening of low nitrogen tolerant maize based on multiple traits at the seedling stage. PeerJ 10:e14218 https://doi.org/10.7717/peerj.14218
Identification and functional analysis of PIN family genes in Gossypium barbadense
Background PIN proteins are an important class of auxin polar transport proteins that play an important regulatory role in plant growth and development. However, their characteristics and functions have not been identified in Gossypium barbadense. Methods PIN family genes were identified in the cotton species G. barbadense, Gossypium hirsutum, Gossypium raimondii, and Gossypium arboreum, and detailed bioinformatics analyses were conducted to explore the roles of these genes in G. barbadense using transcriptome data and quantitative reverse-transcription polymerase chain reaction (qRT-PCR) technology. Functional verification of the genes was performed using virus-induced gene silencing (VIGS) technology. Results A total of 138 PIN family genes were identified in the four cotton species; the genes were divided into seven subgroups. GbPIN gene family members were widely distributed on 20 different chromosomes, and most had repeated duplication events. Transcriptome analysis showed that some genes had differential expression patterns in different stages of fiber development. According to ‘PimaS-7’ and ‘5917’ transcript component association analysis, the transcription of five genes was directly related to endogenous auxin content in cotton fibers. qRT-PCR analysis showed that the GbPIN7 gene was routinely expressed during fiber development, and there were significant differences among materials. Transient silencing of the GbPIN7 gene by VIGS led to significantly higher cotton plant growth rates and significantly lower endogenous auxin content in leaves and stems. This study provides comprehensive analyses of the roles of PIN family genes in G. barbadense and their expression during cotton fiber development. Our results will form a basis for further PIN auxin transporter research.
Long et al. (2022) Identification and functional analysis of PIN family genes in Gossypium barbadense. PeerJ 10:e14236 https://doi.org/10.7717/peerj.14236
Artificial light at night correlates with seabird groundings: mapping city lights near a seabird breeding hotspot
Artificial light at night (ALAN) is a growing conservation concern for seabirds, which can become disoriented and grounded by lights from buildings, bridges and boats. Many fledgling seabirds, especially Procellariiformes such as petrels and shearwaters, are susceptible to light pollution. The Hauraki Gulf, a seabird hotspot located near Tāmaki Makaurau/Auckland, Aotearoa—New Zealand’s largest urban city, with a considerable amount of light pollution and regularly documented events of seabird groundings. We aim to identify the characteristics of locations especially prone to seabird groundings. We used an online database of seabirds taken to a wildlife rescue facility by the public to map 3 years of seabird groundings and test for correlations between seabird groundings and the natural night sky brightness. We found that areas with lower amounts of natural night sky brightness and greater light pollution often had a higher number of seabirds grounded. Further, we identified important seasonal patterns and species differences in groundings. Such differences may be a by-product of species ecology, visual ecology and breeding locations, all of which may influence attraction to lights. In general, seabird groundings correlate with the brightness of the area and are species-specific. Groundings may not be indicative of human or seabird population abundance considering some areas have a lower human population with high light levels and had high amounts of seabird groundings. These findings can be applied worldwide to mitigate groundings by searching and targeting specific brightly lit anthropogenic structures. Those targeted structures and areas can then be the focus of light mitigation efforts to reduce seabird groundings. Finally, this study illustrates how a combination of community science, and a concern for seabirds grounded from light attraction, in addition to detailed animal welfare data and natural night sky brightness data can be a powerful, collaborative tool to aid global conservation efforts for highly-at-risk animals such as seabirds.
Heswall et al. (2022) Artificial light at night correlates with seabird groundings: mapping city lights near a seabird breeding hotspot. PeerJ 10:e14237 https://doi.org/10.7717/peerj.14237
Terrien, a metabolite made by Aspergillus terreus, has activity against Cryptococcus neoformans
Antimicrobial compounds, including antibiotics, have been a cornerstone of modern medicine being able to both treat infections and prevent infections in at-risk people, including those who are immune-compromised and those undergoing routine surgical procedures. Their intense use, including in people, animals, and plants, has led to an increase in the incidence of resistant bacteria and fungi, resulting in a desperate need for novel antimicrobial compounds with new mechanisms of action. Many antimicrobial compounds in current use originate from microbial sources, such as penicillin from the fungus Penicillium chrysogenum (renamed by some as P. rubens). Through a collaboration with Aotearoa New Zealand Crown Research Institute Manaaki Whenua–Landcare Research we have access to a collection of thousands of fungal cultures known as the International Collection of Microorganisms from Plants (ICMP). The ICMP contains both known and novel species which have not been extensively tested for their antimicrobial activity. Initial screening of ICMP isolates for activity against Escherichia coli and Staphylococcus aureus directed our interest towards ICMP 477, an isolate of the soil-inhabiting fungus, Aspergillus terreus. In our investigation of the secondary metabolites of A. terreus, through extraction, fractionation, and purification, we isolated nine known natural products. We evaluated the biological activity of selected compounds against various bacteria and fungi and discovered that terrein (1) has potent activity against the important human pathogen Cryptococcus neoformans.
Cadelis et al. (2022) Terrien, a metabolite made by Aspergillus terreus, has activity against Cryptococcus neoformans. PeerJ 10:e14239 https://doi.org/10.7717/peerj.14239
Fecal fungal microbiota alterations associated with clinical phenotypes in Crohn’s disease in southwest China
Although previous studies reported that gut fungal microbiota was associated with Crohn’s disease (CD), only a few studies have focused on the correlation between gut fungi and clinical phenotypes of CD. Here, we aimed to analyze the association between intestinal fungi and the occurrence of CD, disease activity, biological behaviors, and perianal lesions. Stool samples from subjects meeting the inclusion and exclusion criteria were collected for running internal transcribed spacer 2 (ITS2) high-throughput sequencing. Then, correlation analysis was conducted between intestinal fungi and different clinical groups. There were 45 patients with CD and 17 healthy controls (HCs) enrolled. Results showed that two phyla, Rozellomycota and Mortierellomycota, were not present in patients with CD compared to HCs. At the same time, there was a higher abundance of fungal genera and species belonging to the phylum Ascomycota in patients with CD. SparCC network analysis showed fewer interactions among the fungal communities in patients with CD compared to HCs. Exophiala dermatitidis was positively associated with the clinical active stage and platelet count. The genus Candida was with significantly higher abundance in the non-B1 CD group based on the Montreal classification. Clonostachys, Humicola, and Lophiostoma were significantly enriched in patients with CD with perianal lesions. Our results demonstrated that the composition of the intestinal fungal microbiota in patients with CD and HCs was markedly different, some of which might play a pathogenic role in the occurrence of CD and perianal lesions. Exophiala dermatitidis and genus Candida might be associated with active disease stage and type non-B1 CD (CD with intestinal stenosis or penetrating lesions, or both), respectively.
Zeng et al. (2022) Fecal fungal microbiota alterations associated with clinical phenotypes in Crohn’s disease in southwest China. PeerJ 10:e14260 https://doi.org/10.7717/peerj.14260