bluuebunny/crossref_metadata_2025 huggingface dataset:
Cryptic lineages, cryptic barriers: historical seascapes and oceanic fronts drive genetic diversity in supralittoral rockpool beetles (Coleoptera: Hydraenidae)
Authors: Villastrigo Adrián , Bilton David T , Abellán Pedro , Millán Andrés , Ribera Ignacio , Velasco Josefa
Published: March 2022

Morphologically cryptic lineages confound many estimates of global biodiversity and are often discovered in ecologically specialized taxa, subject to strong morphological constraint. Such a situation may apply in many extreme environments, including supralittoral rockpools, where dramatic fluctuations in water availability and salinity impose strong selection pressures on the inhabitants. Here we explore the genetic diversity and phylogeography of supralittoral rockpool Ochthebius beetles in the eastern Atlantic and western Mediterranean, using a combination of mitochondrial and nuclear markers and dense geographical sampling of the three recognized widespread species. Our results point to the existence of morphologically cryptic lineages within all currently named taxa and suggest that the distribution of these is linked to both historical and contemporary marine hydrogeography; a combination of ocean currents and winds apparently driving the spatial patterns observed. The main contemporary barrier to dispersal for Ochthebius is located around the Ibiza Channel, whilst the Messinian Salinity Crisis appears to have been the ultimate driver of lineage diversification in these insects. Our results show that oceanographic processes do not just shape the evolution of fully marine species, but also impact significantly on the terrestrially derived inhabitants of the coastal zone.
Differentiation of Palm-Infecting Phytoplasmas in the Caribbean Basin Using High Resolution Melt Curve Analysis of the secA Gene
Authors: Bloch Melody , Helmick Ericka E. , Bahder Brian W.
Published: March 2022

Palm lethal decline is a disease that is always fatal to infected palm hosts and is caused by three species of phytoplasma in the Caribbean basin: ‘Candidatus Phytoplasma palmae’, ‘Ca. P. aculeata’, and ‘Ca. P. hispanola’. Movement of these pathogens throughout the Caribbean has been documented since their discovery in Jamaica. Over time, means of confirming infections in palms have improved. Current protocols utilize quantitative PCR (qPCR) for rapid amplification and distinction of these phytoplasmas using TaqMan probes and high-resolution melt-curve analysis (HRMA) of the 16S rRNA gene. These assays either do not detect all three phytoplasmas (HRMA) or do not distinguish between the three (TaqMan). In this study, a new qPCR-HRMA assay is developed that amplifies and distinguishes all three phytoplasmas currently known to kill palms in the Caribbean. Efficiency for the primer set secA614_F/secA759_R was shown to be consistent for all species at each concentration and yielded distinct melting temperature ranges for amplicons of ‘Ca. P. palmae’ (73.3 to 73.4°C), ‘Ca. P. aculeata’ (72.9 to 73.0°C), and ‘Ca. P. hispanola’ (73.5 to 73.6°C). This assay is a useful new tool not only for diagnostics that will contribute to monitoring and management programs, but it will also aid in basic research by allowing rapid screening of large samples in the context of vector surveys or identification of reservoir hosts.
Sensitivity of Colletotrichum acutatum Species Complex from Strawberry to Fungicide Alternatives to Quinone-Outside Inhibitors
Authors: Rebello Carolina S. , Baggio Juliana S. , Forcelini Bruna B. , Peres Natalia A.
Published: March 2022

Colletotrichum acutatum is a species complex that causes anthracnose fruit rot and root necrosis on strawberry. The major and minor species within the complex that affect strawberry production are C. nymphaeae and C. fioriniae, respectively. The disease can significantly reduce yield under conducive weather, and its management has greatly relied on quinone-outside inhibitor fungicides (QoI). However, due to the emergence of resistant isolates, such products are no longer effective. Therefore, alternative fungicides were investigated. C. nymphaeae and C. fioriniae isolates were collected from multiple strawberry fields in the United States from 1995 to 2017. The sensitivity of benzovindiflupyr, penthiopyrad, pydiflumetofen, fluazinam, fludioxonil, and cyprodinil was assessed by in vitro and in vivo assays. Both Colletotrichum species were sensitive to benzovindiflupyr, penthiopyrad, fluazinam, and fludioxonil based on mycelial growth assays. Interestingly, of these products, only penthiopyrad did not inhibit conidial germination at 100 µg/ml. For cyprodinil, C. nymphaeae was sensitive based on the mycelial growth, whereas C. fioriniae was not inhibited. Neither species was inhibited by pydiflumetofen in mycelial growth, conidial germination, nor detached fruit assays. The prepackaged mixtures fludioxonil + cyprodinil and fludioxonil + pydiflumetofen were effective in a field trial; however, their use should be carefully considered because of the lack of efficacy of one of the compounds in the mixture. This study sheds light on the potential registration of products alternative to QoIs, such as benzovindiflupyr and fluazinam, which could improve the management of strawberry anthracnose.
Identification of Quantitative Trait Loci Associated with Bacterial Leaf Spot Resistance in Baby Leaf Lettuce
Authors: Sthapit Kandel Jinita , Sandoya Germán V. , Zhou Wei , Read Quentin D. , Mou Beiquan , Simko Ivan
Published: March 2022

Spring mix is a popular packaged salad that contains lettuce (Lactuca sativa L.) as one of its main ingredients. Plants for baby leaf lettuce (BLL) production are grown at very high densities, which enhances the occurrence of bacterial leaf spot (BLS) caused by Xanthomonas hortorum pv. vitians (Xhv), a disease that can make the crop unmarketable. The market demands disease-free, high-quality BLL all year round. Growing highly BLS-resistant cultivars will reduce loss of yield and quality, thus minimizing economic detriment to lettuce and spring mix growers. The research objectives were to identify lettuce accessions resistant to BLS and associated quantitative trait loci (QTL). A total of 495 lettuce accessions were screened with six isolates (BS0347, BS2861, BS3127, L7, L44, and Sc8B) of Xhv. Accessions showing overall high-level resistance to all tested Xhv isolates were ‘Bunte Forellen’, PI 226514, ‘La Brillante’, ARM09-161-10-1-4, ‘Grenadier’, ‘Bella’, PI 491210, ‘Delight’, and ‘Romana Verde del Mercado’. Genome-wide association studies of BLS resistance by mixed linear model analyses identified significant QTLs on four lettuce chromosomes (2, 4, 6, and 8). The most significant QTL was on Chromosome 8 (P = 1.42 × 10−7), which explained 6.7% of total phenotypic variation for the disease severity. Accessions with a high level of resistance detected in this study are valuable resources for lettuce germplasm improvement. Molecular markers closely linked to QTLs can be considered for marker-assisted selection to develop new BLL lettuce cultivars with resistance to multiple races of Xhv.
Assessment of Selected Commercially Available Seed Treatments on Suppressing the Effects of Red Crown Rot on Soybeans Under a Controlled Environment
Authors: Kleczewski Nathan , Geisler Seth
Published: March 2022

Calonectria ilicicola is a soilborne fungus responsible for red crown rot (RCR) in soybeans. Recently, this disease has been detected in new areas within the United States and Asia, where it has been reported to cause significant yield losses. To date, no data on the efficacy of fungicide seed treatments for suppressing RCR in soybeans are available. We screened three commercially available soybean seed treatments (Acceleron STANDARD; Acceleron STANDARD + IleVO; Cruiser MAXX + Saltro) for impacts on germination, seedling growth, and disease caused by C. ilicicola under controlled laboratory conditions. The Cruiser MAXX + Saltro treatment improved final plant dry mass to levels similar to noninoculated controls. Both Acceleron STANDARD + IleVO and Cruiser MAXX + Saltro reduced percent root rot. Acceleron STANDARD alone did not impact root rot, indicating that the IleVO component was efficacious on C. ilicicola. These data indicate that IleVO and Cruiser MAXX + Saltro have potential for reducing early season impacts of RCR in soybeans. Future work assessing these seed treatments in field-grown soybeans is needed to better understand the role of seed treatments as components of an integrated management program for RCR.
Mechanisms of GZ17-6.02 resistance
Authors: Booth Laurence , West Cameron , Von Hoff Daniel , Dent Paul
Published: March 2022

Objectives

The drug GZ17-6.02 is undergoing phase I in solid tumor patients (NCT03775525). The present studies initially determined the impact of prolonged exposure of colorectal tumors to GZ17-6.02, and to determine whether GZ17-6.02 enhanced the efficacy of an anti-PD1 antibody. Subsequently, studies defined the evolutionary resistance mechanisms in tumor cells previously exposed to GZ17-6.02.

Methods

IACUC-approved animal studies were performed. In cell immunoblotting, cell transfections and trypan blue death assays were performed.

Results

Prolonged exposure of colorectal tumors to GZ17-6.02 enhanced the efficacy of 5-fluorouracil and of an anti-PD1 antibody, significantly prolonging animal survival. Tumor cells previously exposed to GZ17-6.02 in vivo had elevated their expression of ERBB2 and ERBB3, and increased phosphorylation of ERBB1, ERBB3, PDGFRβ, AKT T308, ERK1/2, p70 S6K T389, STAT5 Y694 and c-SRC Y416. The phosphorylation of c-SRC Y527 declined. The efficacy of ERBB receptor inhibitors at killing these resistant tumor cells was unaltered by prior GZ17-6.02 exposure whereas the efficacy of multi-kinase/PDGFRβ inhibitors was significantly reduced. Treatment of colon cancer cells with GZ17-6.02 rapidly reduced the levels of multiple HDAC proteins and altered their subcellular localization. Isolates from resistant tumors expressed less CD95 and FAS-L. HDAC inhibitors enhanced CD95 and FAS-L levels in the resistant cells via activation of NFκB and HDAC inhibitors restored the efficacy of GZ17-6.02 to near control levels.

Conclusions

Our findings demonstrate that GZ17-6.02 has the potential to be developed as a colon cancer therapeutic and that resistance to the drug can be partially reversed by HDAC inhibitors.
Expression and clinical significance of CXCL17 and GPR35 in endometrial carcinoma
Authors: Hao Jun , Gao Xiang , Wang Ya-ping , Liu Qing , Zhu Hai , Zhao Shu-jun , Qin Qiao-hong , Meng Jie , Li Lin-Lin , Lin Shao-Chong , Song Zhenzhen , Li Hongyu
Published: March 2022

Endometrial carcinoma is one of the most common gynecologic malignancies. CXCL17-CXCR8 (GPR35) axis is reported to play an indispensability role in tumors. Our purpose is to screen possible prognostic and immune-related factors in endometrial carcinoma by detecting the mRNA and protein expression of CXCL17 and CXCR8. We use the qRT-PCR method to test the mRNA expression of CXCL17 and CXCR8 in 35 pairs of endometrial carcinoma and adjacent tissue. The protein expression of CXCL17 and CXCR8 in 30 cases of normal proliferative endometrium, 30 cases of endometrial atypical hyperplasia and 50 cases of endometrial carcinoma was detected by tissue microarray immunohistochemistry. There was no significant difference in the positive expression rate between endometrial adenocarcinoma tissue and endometrial atypical hyperplasia tissue (P > 0.05). But significantly better than normal proliferative tissue (P < 0.001). Correlation analysis of CXCR8 and CXCL17 in endometrial carcinoma showed a positive correlation (r = 0.9123, P < 0.0001). For patients with endometrial cancer, the overall survival (OS) of patients with high CXCL17 expression was significantly higher than that low CXCL17 expression (log-rank test, P < 0.0001), whereas CXCR8 had no statistical significance. But the expression of CXCR8 is an independent prognostic factor of OS in endometrial carcinoma patients. Our study showed that CXCL17 and CXCR8 may be involved in the occurrence and development of endometrial cancer. High expression of CXCL17 may be used as a biomarker for predicting survival. Because CXCL17 and CXCL18 are related to lymphocytes and immune regulation, they are expected to become potential targets for immunotherapy.
LncRNA ZFPM2-AS1 drives the progression of nasopharyngeal carcinoma via modulating the downstream miR-3612/DTL signaling
Authors: Chang Xiaojing , Jian Lei
Published: March 2022

LncRNA ZFPM2-AS1 has been illuminated to function as a carcinogenic driver in various human cancers. Whereas, the role of ZFPM2-AS1 in nasopharyngeal carcinoma (NPC) remains puzzled. To further understand NPC pathogenesis, we investigated the regulatory effects of ZFPM2-AS1 in NPC. Expression analysis for ZFPM2-AS1, miR-3612 and denticleless E3 ubiquitin protein ligase homolog (DTL) mRNA was carried out using real-time quantitative PCR. For the expression analysis of DTL protein, a western blot assay was applied. Cell proliferation was ascertained using the cell counting kit-8 assay and colony formation assay. Cell apoptosis was estimated based on the expression levels of BCL2-Associated X and B-cell lymphoma-2 using western blot assay. To verify the role of ZFPM2-AS1, a Xenograft model was prepared in vivo. The underlying binding between miR-3612 and ZFPM2-AS1 or DTL was validated through dual-luciferase-reporter assay or protein immunoprecipitation assay. ZFPM2-AS1 showed upregulated expression in NPC samples and cells. Meanwhile, ZFPM2-AS1 was mainly located in the cytoplasm. Knockdown of ZFPM2-AS1 restrained NPC cell proliferation and induced apoptosis, as well as suppressed tumorigenesis in animal models. ZFPM2-AS1 targeted miR-3612 whose expression was decreased in NPC samples and cells. Repression of miR-3612 aggravated NPC cell development and largely reversed the functional role of ZFPM2-AS1 silencing on NPC cell growth. MiR-3612 directly interacted with DTL, and DTL expression was upregulated in NPC. Downregulation of DTL blocked NPC cell growth, while miR-3612 inhibition partly abrogated the effects of DTL knockdown. ZFPM2-AS1 knockdown considerably restrained NPC development via targeting the miR-3612/DTL signaling. The study provided new insights to understand NPC pathogenesis.
Circular RNA sterile alpha motif domain containing 4A contributes to cell 5-fluorouracil resistance in colorectal cancer by regulating the miR-545-3p/6-phosphofructo-2-kinase/fructose-2,6-bisphosphataseisotype 3 axis
Authors: Gao Yang , Liu Chen , Xu Xiaoyun , Wang Yijing , Jiang Yuanyuan
Published: March 2022

Colorectal cancer (CRC) is one of the most fatal cancers in the world. Circular RNA sterile alpha motif domain containing 4A (circSAMD4A) was found to be highly expressed in CRC and promoted the tumorigenesis of CRC. However, the role of circSAMD4A in 5-fluorouracil (5-Fu) resistance of CRC is yet to be clarified. This study is designed to investigate the function of circSAMD4A in 5-Fu resistance of CRC and its potential molecular mechanism. Quantitative real-time PCR was used to detect the expression levels of circSAMD4A, 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase isotype 3 (PFKFB3) mRNA, and miR-545-3p, and western blot was used to detect the protein expression. For functional analysis, 3-(4, 5-dimethylthiazol-2-yl)-2, 5-diphenyltetrazolium bromide assay, colony formation/5-ethynyl-2′-deoxyuridine assay, flow cytometry analysis, and glycolysis metabolism analysis were used to assess the capacities of cell viability, proliferation, apoptosis, and glycolysis in 5-Fu–resistant cells of CRC. The dual-luciferase reporter assay was used to verify the interaction between miR-545-3p and circSAMD4A or PFKFB3. Xenograft tumor model was established to confirm the biological role of circSAMD4A in 5-Fu resistance of CRC in vivo. CircSAMD4A was upregulated in 5-Fu–resistant CRC tissues and cells. Functionally, circSAMD4A knockdown inhibited the proliferation and glycolysis mechanism but promoted apoptosis in 5-Fu–resistant cells of CRC. CircSAMD4A was identified as a molecular sponge of miR-545-3p to upregulate PFKFB3 expression. Mechanistically, circSAMD4A knockdown-induced 5-Fu sensitivity was mediated by miR-545-3p/PFKFB3 axis. Moreover, circSAMD4A knockdown improved 5-Fu sensitivity of CRC in vivo. CircSAMD4A contributed to 5-Fu resistance of CRC cells partly through upregulating PFKFB3 expression by sponging miR-545-3p, providing a possible circRNA-targeted therapy for CRC.
Circ_0003146 upregulates SCARB1 expression by acting as a miR-1272 sponge to promote malignant behaviors of clear cell renal cell carcinoma
Authors: Xia Zongyu , Wang Qin , Lu Peng
Published: March 2022

Circular RNAs (circRNAs) exhibit essential regulation in the malignant development of clear cell renal cell carcinoma (ccRCC). The aims of this study were to investigate the role and mechanism of circ_0003146 in the biologic behaviors of ccRCC. RNA level analysis was performed through reverse transcription-quantitative PCR assay. Cell proliferation was measured by EdU assay and cell counting kit-8 assay. The protein expression was analyzed using a western blot. Flow cytometry and caspase 3 activity assay were used to assess cell apoptosis. Cell migration and invasion were evaluated via wound healing assay and transwell assay. Circ_0003146 function in vivo was determined by xenograft tumor assay. Dual-luciferase reporter assay was applied for target relation analysis. Circ_0003146 upregulation was detected in ccRCC tissues and cells. Downregulation of circ_0003146 induced inhibition of proliferation, migration, invasion and EMT but the promotion of apoptosis in ccRCC cells. Tumor growth in vivo was inhibited after knockdown of circ_0003146. Circ_0003146 directly interacted with miR-1272, and the miR-1272 sponging effect was responsible for the function of circ_0003146. Scavenger receptor class B type 1 (SCARB1) was a target of miR-1272, and circ_0003146 regulated SCARB1 level by absorbing miR-1272. The regulation of circ_0003146 in ccRCC progression was achieved by upregulating SCARB1 in part. The current findings demonstrated that circ_0003146 contributed to the malignant progression of ccRCC via inducing SCARB1 upregulation by targeting miR-1272.
Inhibiting nonhomologous end-joining repair would promote the antitumor activity of gemcitabine in nonsmall cell lung cancer cell lines
Authors: Guo Nannan , Li Shaojun , Liu Bo , Chen Ping , Li Jingbo , Zhao Yunlong , Zhao Yingnan , Tang Jian , Zhang Wen
Published: March 2022

Nonsmall cell lung cancer (NSCLC) is a major type of lung cancer. In current study, we aim to evaluate whether the combination of Ku70/80 heterodimer protein inhibitor STL127705 and gemcitabine would be more favorable approach for the treatment of NSCLC compared with monotreatment with gemcitabine. Clongenic survival assay was used to determine the survival and sensitivity to irradiation. H1299 was stained with fluorescein isothiocyanate-Annexin V, and cell apoptosis was measured by flow cytometry. H1299 cells were transfected with nonhomologous end-joining (NHEJ) repair reporter, and stable cell line was selected by puromycin. NHEJ activity was determined based on the intensity of green fluorescent protein. DNA double-strand breaks (DSBs) were determined by the fluorescence intensity of γH2AX using flow cytometry. The mRNA expressions of Ku70 and Ku80 were determined using quantitative real-time PCR. Combination of STL127705 enhanced sensitivity of NSCLC cell lines to irradiation when compared with treatment with gemcitabine alone. However, small cell lung cancer cell line was not affected. H1299 cells treated with STL127705 in combination with gemcitabine showed a significantly increased apoptosis compared with H1299 cells treated with gemcitabine alone. Moreover, STL127705 treatment dramatically reduced NHEJ activity in H1299 cells when compared with gemcitabine single treatment. Increased DSBs were consistently observed in H1299 when treated with the combination of STL127705 and gemcitabine. However, the mRNA levels of Ku70 and Ku80 were upregulated by the combination treatment. It demonstrated that STL127705 enhanced antitumor activity of gemcitabine. Mechanistically, treatment with STL127705 enhanced DNA damage via inhibiting NHEJ pathway, blocking DNA-PK, and forming Ku70/80 heterodimer, eventually leading to tumor cells apoptosis.
Efficacy and safety of lurasidone in schizophrenia: pooled analysis of European results from double-blind, placebo-controlled 6-week studies
Authors: Calisti Fabrizio , Cattaneo Agnese , Calabrese Mariangela , Mao Yongcai , Tocco Michael , Pikalov Andrei , Goldman Robert
Published: March 2022

The objective of this study is to confirm the efficacy and safety of lurasidone in the acute treatment of schizophrenia in European patients. Data were pooled from three studies of patients randomized to 6 weeks of double-blind, placebo-controlled, fixed-dose (40/80 mg and 120/160 mg) lurasidone. The primary efficacy endpoint was a week 6 change in the Positive and Negative Syndrome Scale (PANSS) total score and secondary endpoints included the Clinical Global Impression, Severity scale (CGI-S). In total 328 safety patients were enrolled; 72.6% were completers. Endpoint change was significantly greater in patients treated with 40–80 mg/d and 120–160 mg/d compared to placebo on the PANSS total score (P < 0.001) and the CGI-Severity score (P < 0.001) for all comparisons. For PANSS total scores, endpoint effect sizes for lurasidone 40–80 mg/d and 120–160 mg/d were 0.68 to 0.77, respectively. Adverse events with a frequency ≥5% (and were greater than for combined lurasidone) were insomnia (11.7%), akathisia (11.3%), headache (7.4%), Parkinsonism (6.5%) and nausea (5.7%). Median changes (in mg/dL) at endpoint were minimal for total cholesterol (−8.0); triglycerides (−8.5) and glucose (−2.0) and in mean weight (−0.2 kg). In European patients with schizophrenia, short-term treatment with lurasidone in doses of 40–160 mg/d was generally safe, well-tolerated and effective with minimal effects on weight and metabolic parameters.
Cold stress upregulates the expression of heat shock and Frost genes, but the evolution of cold stress resistance is apparently not mediated through either heat shock or Frost genes in the cold stress selected populations of Drosophila melanogaster
Authors: Singh Karan , Prasad Nagaraj Guru
Published: March 2022

The ability to thermal adaptation can alter insects’ reproductive traits and physiologic response. A number of studies in Drosophila documented the higher expression levels of heat shock proteins (Hsps) and Frost (Fst) genes during the recovery phase of cold shock treatment and suggested that higher expression levels of these genes and lipids can protect from cold stress. However, these genes’ expression and cold adaptation have not been well studied. Therefore, understanding the molecular and biochemical basis of cold adaptation, we examined the levels of lipid and expression patterns of Hsp22, Hsp23, Hsp40, Hsp68, Hsp70, Hsp 83, and Fst genes under the cold stress or benign condition in the populations of Drosophila melanogaster selected for increased resistance to cold shock.

We observed the significant up-regulation of Hsp22, Hsp23, Hsp40, Hsp68, and Fst genes in the FSB and FCB populations during the recovery phase post cold shock compared to the no shock condition. However, there was not a significant change in the transcript levels of these genes between FSB and FCB under both the cold stress or no shock condition. Additionally, we noticed higher total lipid levels in the females from cold shock treatment than those from no shock treatment. This finding suggests that cold selected populations have different mechanisms to sustain cold stress.
TP63-TRIM29 axis regulate enhancer methylation and chromosomal instability in prostate cancer
Authors: Sultanov R. , Mulyukina A. , Zubkova O. , Fedoseeva A. , Bogomazova A. , Klimina K. , Larin A. , Zatsepin T. , Prikazchikova T. , Sharova E. , Generozov E. , Govorun V. , Lagarkova M. , Arapidi G.
Published: March 2022

Abstract

Prostate adenocarcinoma (PRAD) is the second most common cause of cancer-related deaths in men. PRAD is often characterized by DNA methylation variability and a high rate of large genomic rearrangements. To elucidate the reasons behind such high variance, we used weighted gene co-expression network analysis for integration RNA-seq, DNA methylation and copy number alterations data from The Cancer Genome Atlas PRAD. Our results show that only a single cluster of co-expressed genes is associated with genomic and epigenomic instability. Within this cluster, TP63 and TRIM29 are key transcription regulators. We revealed that TP63 regulates the level of enhancer methylation in prostate basal epithelium cells. TRIM29 forms a complex with TP63 and together regulate the expression of genes specific to the prostate basal epithelium. Moreover, TRIM29 binds DNA repair proteins and prevents formation of the TMPRSS2:ERG gene fusion typically observed in PRAD. Therefore, the study shows that TRIM29 and TP63 are important regulators maintaining the identity of the basal epithelium under physiological conditions. Finally, we uncover the role of TRIM29 in PRAD development.
Ketones facilitate transcriptional resolution of secondary DNA structures in premature aging
Authors: Petr Michael Angelo , Carmona-Marin Lina M , Tulika Tulika , Kristensen Stella , Reves Simon , Bakula Daniela , Keijzers Guido , Osborne Brenna , Mitchell Sarah J , Hamilton Sam , Kato Jonathan , Alfaras Irene , Teklu Amanuel A. , Heckenbach Indra , Madsen Jakob , Ezra Michael Ben , Mkrtchyan Garik , Varner Erika , Fink Benjamin , Krusenstiern Eliana von , Snyder Nathaniel W , Herranz Hector , Cabo Rafael de , Scheibye-Knudsen Morten
Published: March 2022

There is currently no established intervention for Cockayne syndrome, a disease characterized by progressive early onset neurodegeneration with features of premature aging. Here, we tested if acetyl-CoA precursors, citrate and beta-hydroxybutyrate, could reduce features of Cockayne syndrome in three model systems. We identified the gene Helicase 89B as a homologue of CSB in drosophila and found that the ketone beta-hydroxybutyrate rescued features of premature aging in Hel89B deficient flies. In mammals, loss of the citrate carrier Indy exacerbated the phenotype of Csbm/m mice which was rescued by a ketogenic diet. The rescue effect appeared to be mediated through ketone stimulated histone acetylation and facilitation of transcriptional readthrough of secondary DNA structures. These findings link a ketogenic diet with transcriptional resolution of secondary structures and DNA repair.
Identifying commonalities between cell lines and tumors at the single cell level using Sobolev Alignment of deep generative models
Authors: Mourragui Soufiane M.C. , Siefert Joseph C. , Reinders Marcel J.T. , Loog Marco , Wessels Lodewyk F.A.
Published: March 2022

Preclinical models are essential to cancer research, however, key biological differences with patient tumors result in reduced translatability to the clinic and high attrition rates in drug development. Variability among and between patients, preclinical models, and individual cells obscures commonalities which could otherwise be exploited therapeutically. To discover the shared biological processes between cell line models and clinical tumors we developedSobolev Alignment, a computational framework which uses deep generative models to capture non-linear processes in single-cell RNA sequencing data and kernel methods to align and interpret these processes. We show that our approach faithfully captures shared processes on a set of three synthetic datasets. Exploiting two large panels of untreated non-small cell lung cancer cell lines and patients, we identify the similarities between cell lines and tumors and show the conservation of key mitotic and immune-related pathways. Employing our approach on a large in-vitro perturbation screen, we show that processes captured by our method faithfully recapitulate the known modes of action of clinically approved drugs and allow investigation into the mode of action of an uncharacterized drug.
Experience does not change the importance of wind support for migratory route selection by a soaring bird
Authors: Brønnvik Hester , Safi Kamran , Vansteelant Wouter M. G. , Byholm Patrik , Nourani Elham
Published: March 2022

Migration is a complex behavior that is costly in terms of time, energy, and risk of mortality. Thermal soaring birds rely on airflow, specifically wind support and uplift, to offset their energetic costs of flight. Their migratory routes are a record of movement decisions to negotiate the atmospheric environment and achieve efficiency. Because thermal soaring is a complex flight type that young birds need to learn, we expected that, as individuals gain more experience, their movement decisions will also increasingly favor the best thermal uplift conditions. We quantified how route choice during autumn migration of young European honey buzzards (Pernis apivorus) was adjusted to wind support and uplift over up to four years of migration and compared this to the choices of adult birds. We found that wind support was important in all migrations. However, we did not find an increase in the use of thermal uplifts, which could be an artifact of the uplift proxies that we used. Age-specific variations in response to airflow might occur at a smaller spatio-temporal scale than we investigated.
Integrative analysis of genomic and transcriptomic alterations of AGR2 and AGR3 in cancer
Authors: Fessart Delphine , Villamor Ines , Chevet Eric , Delom Frederic , Robert Jacques
Published: March 2022

The AGR2 and AGR3 genes have been shown by numerous groups to be functionally associated to adenocarcinoma progression and metastasis. We explore in this paper the data available in databases concerning genomic and transcriptomic features concerning these two genes: the NCBI dbSNP database was used to explore the presence and roles of constitutional SNPs, and the NCI, CCLE and TCGA databases were used to explore somatic mutations and copy number variations (CNVs), as well as mRNA expression of these genes in human cancer cell lines and tumours. Relationships of AGR2/3 expression with whole genome mRNA expression and cancer features (i.e. mutations and CNVs of oncogenes and tumour suppressor genes [TSG]) were established using CCLE and TCGA databases. In addition, the CCLE data concerning CRISPR gene extinction screens (Achilles project) were explored concerning these two genes and a panel of oncogenes and TSG. We observed that no functional polymorphism or recurrent mutation could be detected in AGR2 or AGR3. The expression of these genes was positively correlated with the expression of epithelial genes and inversely correlated with that of mesenchymal genes. It was also significantly associated with several cancer features, such as TP53 or SMAD4 mutations, depending on the gene and the cancer type. The CRISPR screens revealed in addition the absence of cell fitness modification upon gene extinction, in contrast to oncogenes (cell fitness decrease) and TSG (cell fitness increase). Overall, these explorations revealed that AGR2 and AGR3 proteins appear as common non-genetic evolutionary factors in the process of human tumorigenesis.
How does the mode of evolutionary divergence affect reproductive isolation?
Authors: De Sanctis Bianca , Schneemann Hilde , Welch John J.
Published: March 2022

When divergent populations interbreed, the outcome will be affected by the genomic and phenotypic differences that they have accumulated. In this way, the mode of evolutionary divergence between populations may have predictable consequences for the fitness of their hybrids, and so for the progress of speciation. To investigate these connections, we present a new analysis of hybridization under Fisher’s geometric model, making few assumptions about the allelic effects that differentiate the hybridizing populations. Results show that the strength and form of postzygotic reproductive isolation (RI) depend on just two properties of the evolutionary changes, which we call the “total amount” and “net effect” of change, and whose difference quantifies the similarity of the changes at different loci, or their tendency to act in the same phenotypic direction. It follows from our results that identical patterns of RI can arise in different ways, since different evolutionary histories can lead to the same total amount and net effect of change. Nevertheless, we show how these estimable quantities do contain some information about the history of divergence, and that – thanks to Haldane’s Sieve – the dominance and additive effects contain complementary information.

Impact Summary

When populations of animals or plants evolve differences in their genomes or traits, the nature of the differences will help to determine whether they can continue to interbreed. For example, the hybrid offspring may be infertile, or unlikely to survive to reproductive age, meaning that the two populations remain distinct from one another even after mating. However, in some cases the hybrids may be more fertile than their parents or have some other reproductive advantage. In this study, we use a mathematical model to relate hybrid fitness to the evolved differences separating the parents. We find that the outcome depends on just two properties of these differences, which capture the “total amount” and the “net effect” of evolutionary change. We then show that different evolutionary divergence scenarios or modes can lead to the exact same hybrid fitness. On the other hand, we can still make some inferences about the history of divergence by observing certain properties of hybrid fitness. Determining the relationship between hybrid fitness and the mode of evolutionary divergence will help to understand how new species form, to plan conservation interventions such as moving individuals between isolated populations to increase their adaptive potential, and to understand how existing species might interact when their habitats overlap, for example due to climate change or other human impacts.
Identification of genetic loci in lettuce mediating quantitative resistance to fungal pathogens
Authors: Pink Harry , Talbot Adam , Graceson Abi , Graham Juliane , Higgins Gill , Taylor Andrew , Jackson Alison C. , Truco Maria , Michelmore Richard , Yao Chenyi , Gawthrop Frances , Pink David , Hand Paul , Clarkson John P. , Denby Katherine
Published: March 2022

Lactuca sativaL. (lettuce) is an important leafy vegetable crop grown and consumed globally. Chemicals are routinely used to control major pathogens, including the causal agents of grey mould (Botrytis cinerea) and lettuce drop (Sclerotinia sclerotiorum). With increasing prevalence of pathogen resistance to fungicides and environmental concerns, there is an urgent need to identify sources of genetic resistance toB. cinereaandS. sclerotiorumin lettuce. We demonstrated genetic variation for quantitative resistance toB. cinereaandS. sclerotiorumin a set of 97 diverse lettuce and wild relative accessions, and between the parents of lettuce mapping populations. Transcriptome profiling across multiple lettuce accessions enabled us to identify genes with expression correlated with resistance, predicting the importance of post-transcriptional gene regulation in the lettuce defence response. We identified five genetic loci influencing quantitative resistance in a F10 mapping population derived from aLactuca serriola(wild relative) x lettuce cross, which each explained 5–10% of the variation. Differential gene expression analysis between the parent lines, and integration of data on correlation of gene expression and resistance in the diversity set, highlighted potential causal genes underlying the quantitative trait loci.

Key Message

We demonstrate genetic variation for quantitative resistance against important fungal pathogens in lettuce and its wild relatives, map loci conferring resistance and predict key molecular mechanisms using transcriptome profiling.
Not optimal, just noisy: the geometry of correlated variability leads to highly suboptimal sensory coding
Authors: Livezey Jesse A. , Sachdeva Pratik S. , Dougherty Maximilian E. , Summers Mathew T. , Bouchard Kristofer E.
Published: March 2022

The brain represents the world through the activity of neural populations. Correlated variability across simultaneously recorded neurons (noise correlations) has been observed across cortical areas and experimental paradigms. Many studies have shown that correlated variability improves stimulus coding compared to a null model with no correlations. However, such results do not shed light on whether neural populations’ correlated variability achieves optimal coding. Here, we assess optimality of noise correlations in diverse datasets by developing two novel null models each with a unique biological interpretation: a uniform correlations null model and a factor analysis null model. We show that across datasets, the correlated variability in neural populations leads to highly suboptimal coding performance according to these null models. We demonstrate that biological constraints prevent many subsets of the neural populations from achieving optimality according to these null models, and that subselecting based on biological criteria leaves coding performance suboptimal. Finally, we show that the optimal subpopulation is exponentially small as a function of neural dimensionality. Together, these results show that the geometry of correlated variability leads to highly suboptimal sensory coding.
Lag-optimized BOLD cerebrovascular reactivity derived from breathing task data has a stronger relationship with baseline cerebral blood flow
Authors: Stickland Rachael C. , Zvolanek Kristina M. , Moia Stefano , Caballero-Gaudes César , Bright Molly G.
Published: March 2022

Cerebrovascular reactivity (CVR) is an important indicator of cerebrovascular health and is commonly studied with the Blood Oxygenation Level Dependent functional MRI (BOLD-fMRI) response to a vasoactive stimulus. There is theoretical and empirical evidence to suggest that baseline cerebral blood flow (CBF) modulates the BOLD signal amplitude, and that baseline CBF may influence BOLD-CVR estimates. We address how some pertinent data acquisition and modelling choices affect the relationship between baseline CBF and BOLD-CVR: whether BOLD-CVR is modelled with breathing task data or just resting-state data, and whether BOLD-CVR amplitudes are optimized for hemodynamic lag effects. For the relationship between baseline CBF and BOLD-CVR, we assessed both between-subject correlations of average GM values and within-subject spatial correlations across cortical regions. Our results suggest that a simple breathing task addition to a resting-state scan, alongside lag-optimization within BOLD-CVR modelling, can improve BOLD-CVR correlations with baseline CBF, both between- and within-subjects, likely because these CVR estimates are more physiologically accurate. We report positive coupling between baseline CBF and BOLD-CVR, both between and within subjects; the physiological explanation of this positive coupling is unclear, and future research with larger sample sizes and more tightly controlled vasoactive stimuli is needed. Understanding how baseline vascular physiology relates to dynamic cerebrovascular processes will bring further insights into what drives between and within subject participant variability in BOLD-CVR measurements and related measurements of cerebrovascular function. These insights are particularly relevant when interpreting results in populations with altered vascular and/or metabolic baselines or impaired cerebrovascular reserve.
Heritable variation in thermoregulation is associated with reproductive success in the world’s largest bird
Authors: Svensson Erik I. , Schou Mads F. , Melgar Julian , Waller John , Engelbrecht Anel , Brand Zanell , Cloete Schalk , Cornwallis Charlie K.
Published: March 2022

Organisms inhabiting extreme thermal environments, such as desert birds, have evolved spectacular adaptations to thermoregulate during hot and cold conditions. However, our knowledge of selection for thermoregulation and the potential for evolutionary responses is limited, particularly for large organisms experiencing extreme temperature fluctuations. Here we use thermal imaging to quantify selection and genetic variation in thermoregulation in ostriches (Struthio camelus), the world’s largest bird species that is experiencing increasingly volatile temperatures. We found that females that are better at regulating their head temperatures (‘thermoregulatory capacity’) had higher egg-laying rates under hotter conditions. Thermoregulatory capacity was both heritable and showed signatures of local adaptation: females originating from more unpredictable climates were better at regulating their head temperatures in response to temperature fluctuations. Together these results reveal that past and present evolutionary processes have shaped genetic variation in thermoregulatory capacity, which appears to protect critical organs, such as the brain, from extreme temperatures during reproduction.

Impact Summary

Large animals inhabiting extreme thermal environments, such as deserts, are predicted to be particularly vulnerable to the increasing temperature fluctuations expected in the future. However, previous work on the evolutionary potential of thermoregulation has primarily focused on the effect of hot temperatures on the survival of small ectotherms. We know little about how large endothermic vertebrates, such as birds, will respond to changing temperatures. Here we study the ostrich (Struthio camelus), the world’s largest bird, that inhabits some of the hottest and driest regions on Earth. We show that the ability of females to reproduce during hot conditions is associated with the regulation of their head temperatures (‘thermoregulatory capacity’). Furthermore, variation in thermoregulation is heritable and related to past climatic conditions: females originating from parts of Africa with more extreme temperature fluctuations were better able to thermoregulate, indicating local adaptation to different climatic conditions. Together, these results suggest that thermoregulation in this large desert bird has evolved in response to past climatic conditions, remains genetically variable and is currently under selection through its effect on reproduction.
Tissue-Restricted Inhibition of mTOR Using Chemical Genetics
Authors: Wassarman Douglas R. , Bankapalli Kondalarao , Pallanck Leo J. , Shokat Kevan M.
Published: March 2022

mTOR is a highly conserved eukaryotic protein kinase that coordinates cell growth and metabolism and plays a critical role in cancer, immunity, and aging. It remains unclear how mTOR signaling in individual tissues contributes to whole-organism processes because mTOR inhibitors, like the natural product Rapamycin, are administered systemically and target multiple tissues simultaneously. We developed a chemical-genetic system, termed selecTOR, that restricts the activity of a Rapamycin analog to specific cell populations through targeted expression of a mutant FKBP12 protein. This analog has reduced affinity for its obligate binding partner FKBP12, which reduces its ability to inhibit mTOR in wild-type cells and tissues. Expression of the mutant FKBP12, which contains an expanded binding pocket, rescues the activity of this Rapamycin analog. Using this system, we show that selective mTOR inhibition can be achieved in S. cerevisiae and human cells, and we validate the utility of our system in an intact metazoan model organism by identifying the tissues responsible for a Rapamycin-induced developmental delay in Drosophila.

Significance Statement

mTOR plays a number of critical organismal roles, including in cell growth, development, immunity and aging, but dissecting the tissue-specific influences of mTOR has proven challenging. This work describes a simple system for identifying the specific tissues and cells responsible for the diverse functions of mTOR, and we show that our system can be used in organisms ranging from yeast to humans.
CD5L constraints acute and systemic inflammation and can be a novel potent therapeutic agent against sepsis
Authors: Oliveira Liliana , Gomes Ana P. , Santos Rita F. , Cardoso Marcos S. , Nóvoa Ana , Luche Hervé , Gartner Fátima , Malissen Bernard , Mallo Moisés , Carmo Alexandre M.
Published: March 2022

The global burden of sepsis, with an estimated 49 million cases and 11 million deaths in 2017, often passes unnoticed to the general public even though it is the direct cause of nearly 20% of all deaths worldwide. This unawareness is perhaps due to misconceptions, or miscoding in the reporting of the ultimate causes of death, as in many diseases it is not the actual infectious agent that causes the biggest harm. Rather, it is the uncontrolled inflammation leading to septic shock that is the most menacing manifestation associated with many infections, and becomes deadly serious once it has passed the stage where anti-microbial drugs no longer have any effect to inactivate or destroy the pathogen. Here we show that the combined anti-bacterial and anti-inflammatory properties of the scavenger receptor cysteine-rich (SRCR) protein CD5L contribute to a remarkable therapeutic effect of the protein to fight sepsis, such that when exogenously administered in C57BL/6 mice with induced lethal-grade sepsis, it can be a very effective curative agent to treat this condition. The resistance conferred by CD5L to polybacterial-induced sepsis using the cecal ligation and puncture (CLP) model is consistent with the reported observations that CD5L physically binds and inactivates diverse species and strains of bacteria. Accordingly, our CD5L-knockout mice are significantly more susceptible to experimentally-induced mid-grade CLP than wild-type animals. We show that CD5L is centered on promoting neutrophil recruitment and activation, overall contributing to reducing the bacteria burden of the animals. However, the dramatic susceptibility of CD5L-deficient animals is not necessarily correlated only with pathogen load, as these mice are also extremely susceptible to sterile sepsis induced by nonlethal doses of LPS. Notwithstanding the observed capacity of CD5L to directly bind to a broad range of pathogens, typical of many PRRs, our evidence suggests that the anti-inflammatory properties of the protein are at least as important as its pathogen-binding potential, and can, and should, be explored to treat the deadly inflammation storm that is sepsis.