Article
Behavioral Sciences
Sylvia Dimitriadou, Eduarda M. Santos, Darren P. Croft, Ronny van Aerle, Indar W. Ramnarine, Amy L. Filby, Safi K. Darden
Summary: This study quantifies the neuroregulatory response of Trinidadian guppies to cooperation or defection by examining the transcriptional response of the oxytocin gene. The results show that individual responses to social partners' behavior depend on individual's predation threat level and experience.
BEHAVIOURAL BRAIN RESEARCH
(2022)
Article
Multidisciplinary Sciences
Endika Haro, Florence Petit, Charmaine U. Pira, Conor D. Spady, Sara Lucas-Toca, Lauren Yorozuya, Austin L. Gray, Fabienne Escande, Anne-Sophie Jourdain, Andy Nguyen, Florence Fellmann, Jean-Marc Good, Christine Francannet, Sylvie Manouvrier-Hanu, Marian A. Ros, Kerby C. Oberg
Summary: Nail-patella syndrome (NPS) is characterized by various symptoms including nail dysplasia, absent/hypoplastic patellae, chronic kidney disease, and glaucoma, and can be caused by haploinsufficiency of LMX1B. However, not all patients with NPS have pathogenic mutations in LMX1B. The study demonstrates that loss-of-function variations in upstream enhancer sequences are responsible for a limb specific form of human NPS.
NATURE COMMUNICATIONS
(2021)
Article
Biotechnology & Applied Microbiology
Gabriel J. Foster, Mackenzie A. C. Sievert, Katrina Button-Simons, Katelyn M. Vendrely, Jeanne Romero-Severson, Michael T. Ferdig
Summary: The use of cyclical regression covariates (CRC) can effectively eliminate the confounding effect of developmentally driven transcriptional changes in clinical samples, leading to reduced errors in transcriptome analysis. This method has immediate application in parasite transcriptome sequencing directly from clinical blood samples and in cost-constrained in vitro experiments.
Article
Biochemistry & Molecular Biology
Mina Noura, Hidemasa Matsuo, Takahiko Yasuda, Shinobu Tsuzuki, Hitoshi Kiyoi, Fumihiko Hayakawa
Summary: TAL1 is frequently dysregulated in T-ALL, and its overexpression is associated with unfavorable clinical outcomes. This study found that the tumor suppressor KLF4 can suppress SE-driven TAL1 expression in T-ALL cells by inhibiting the formation of 5' TAL1 super-enhancer. A small molecule inducer of KLF4, APTO-253, exerts an anti-leukemic effect by targeting SE-driven TAL1 expression in T-ALL cells. Induction of KLF4 may be a promising strategy to control TAL1 expression and could serve as a novel treatment for T-ALL patients with poor prognosis.
Article
Biochemistry & Molecular Biology
Hua Su, Jiahui Xu, Jia Li, Zhenzhen Yi
Summary: The actin gene family is a diverse and ancient eukaryotic cellular cytoskeletal gene family that is essential for many cellular processes. We analyzed the evolutionary pattern of this gene family in ciliates and found that there are ciliate-specific subfamilies of actin genes and the number of actin isoforms varies greatly among ciliate species. The evolution of the actin gene family in ciliates can be explained by the "birth and death" model, and actin genes have been subjected to strong negative selection to maintain their structures and functions.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2023)
Article
Developmental Biology
Katsiaryna Maskalenka, Gokberk Alagoz, Felix Krueger, Joshua Wright, Maria Rostovskaya, Asif Nakhuda, Adam Bendall, Christel Krueger, Simon Walker, Aylwyn Scally, Peter J. Rugg-Gunn
Summary: Gene duplication events contribute to evolution by providing genetic material for new gene functions and allow for the emergence of diverse developmental strategies between species. NANOGP1, a tandem duplicate of the transcription factor NANOG, plays a role in human early development. NANOGP1 and NANOG exhibit overlapping but distinct expression patterns, with NANOGP1 primarily expressed in early epiblast cells and naive pluripotent stem cells.
Article
Oncology
Martin K. Bakht, Yasutaka Yamada, Sheng-Yu Ku, Varadha Balaji Venkadakrishnan, Joshua A. Korsen, Teja M. Kalidindi, Kei Mizuno, Shin Hye Ahn, Ji-Heui Seo, Maria Mica Garcia, Francesca Khani, Olivier Elemento, Henry W. W. Long, Alain Chaglassian, Nagavarakishore Pillarsetty, Jason S. Lewis, Matthew Freedman, Anthony P. Belanger, Quang-De Nguyen, Himisha Beltran
Summary: Beltran and colleagues explore the regulatory roles of HOXB13 and AR in the heterogeneous expression of PSMA in castration-resistant prostate cancer. They found that PSMA expression is lost in a subset of CRPC patients and is influenced by the microenvironment. The study also identifies HOXB13 as an upstream regulator of PSMA, independent of AR expression. These findings provide insights for the development of PSMA-targeted therapies and complementary biomarkers.
Article
Multidisciplinary Sciences
Margarete Diaz-Cuadros, Teemu P. Miettinen, Owen S. Skinner, Dylan Sheedy, Carlos Manlio Diaz-Garcia, Svetlana Gapon, Alexis Hubaud, Gary Yellen, Scott R. Manalis, William M. Oldham, Olivier Pourquie
Summary: Animals display inter-species variation in embryonic development rates, with differences in biochemical reaction rates being thought responsible for species-specific rates. This study establishes an in vitro system using pluripotent stem cells to simulate the twofold difference in developmental rates between mouse and human embryos. The mass-specific metabolic rates were found to scale with developmental rate, higher in mouse cells than in human cells. Manipulating metabolic rates could control developmental rate and have translational applications.
Article
Plant Sciences
Venkata Suresh Bonthala, Benjamin Stich
Summary: Potato is the most important non-grain food crop, and tandem duplication plays a significant role in genome evolution. This study used multiple potato genotypes to investigate the abundance and distribution of tandemly duplicated genes, the bias in functional specificities, the relationship among coding sequence, promoter and expression divergences, and the role of tandem duplication in generating lineage-specific gene families. The results showed that tandemly duplicated genes are dispersed throughout the genome and exhibit different functional enrichments. There is a significant correlation among expression, promoter, and protein divergences in tandemly duplicated genes. The lineage-specific expansion of gene families by tandem duplication, coupled with functional bias, has contributed to potato's genotypic diversity and adaptation to environmental stimuli.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Ecology
Yuwei Wang, Baocheng Guo
Summary: The study found that in zebrafish, ohnologs have fewer AS forms compared to their singleton orthologs, supporting the function-sharing model of AS divergence between duplicates. In stickleback, ohnologs have more AS forms compared to their singleton orthologs, supporting the accelerated model of AS divergence between duplicates. In medaka, the evolution of AS in ohnologs supports a combined scenario of the function-sharing and accelerated model of AS divergence between duplicates.
BMC ECOLOGY AND EVOLUTION
(2021)
Article
Multidisciplinary Sciences
Elizabeth D. Larson, Hideyuki Komori, Tyler J. Gibson, Cyrina M. Ostgaard, Danielle C. Hamm, Jack M. Schnell, Cheng-Yu Lee, Melissa M. Harrison
Summary: The pioneer transcription factor Zelda plays a crucial role in reprogramming germ cells during early Drosophila embryo development. Research further demonstrates that Zelda promotes undifferentiated stem-cell fate in the larval brain, and its ability to define cis-regulatory regions is influenced by cell-type-specific chromatin architecture. It is proposed that Zelda regulates essential transitions in neuroblasts and embryos through a shared gene-regulatory network driven by cell-type-specific enhancers.
NATURE COMMUNICATIONS
(2021)
Article
Plant Sciences
Zhenhao Guo, Lisi He, Xiaobo Sun, Chang Li, Jiale Su, Huimin Zhou, Xiaoqing Liu
Summary: The AP2/ERF gene family is a conserved and important transcription factor family mainly found in plants, with various functions in regulating plant biological and physiological processes. This study focused on the AP2/ERF gene family in Rhododendron simsii, an important ornamental plant, using the existing whole-genome sequence of Rhododendron to investigate the genes on a genome-wide scale. A total of 120 Rhododendron AP2/ERF genes were identified and classified into five main subfamilies. The study also analyzed the expression patterns of these genes and found that they responded to abiotic stresses. This research provides comprehensive information on the AP2/ERF gene family in Rhododendron and lays the foundation for future genetic improvement.
Article
Cell Biology
Alexandros Sountoulidis, Sergio Marco Salas, Emelie Braun, Christophe Avenel, Joseph Bergenstrahle, Jonas Theelke, Marco Vicari, Paulo Czarnewski, Andreas Liontos, Xesus Abalo, Zaneta Andrusivova, Reza Mirzazadeh, Michaela Asp, Xiaofei Li, Lijuan Hu, Sanem Sariyar, Anna Martinez Casals, Burcu Ayoglu, Alexandra Firsova, Jakob Michaelsson, Emma Lundberg, Carolina Waehlby, Erik Sundstroem, Sten Linnarsson, Joakim Lundeberg, Mats Nilsson, Christos Samakovlis
Summary: Sountoulidis et al. have created a spatial gene expression atlas of the human embryonic lung during the first trimester of gestation, identifying 83 cell states and developmental trajectories. They integrated single-cell RNA sequencing and spatially resolved transcriptomics, providing an open platform for interactive exploration. The atlas can serve as a reference for further research and understanding of pulmonary diseases.
NATURE CELL BIOLOGY
(2023)
Article
Genetics & Heredity
Andre Carvalho, Didier Mazel, Zeynep Baharoglu
Summary: The study shows that Vibrio cholerae becomes more tolerant to aminoglycosides when VchM is deleted, likely due to increased synthesis of molecular chaperones.
Article
Biochemistry & Molecular Biology
Yichun Qiu, Claudia Koehler
Summary: MADS-box transcription factors are present in almost all major eukaryotic groups. Type II MADS-box TFs are closely connected to major evolutionary innovations in flowering plants, while the role of Type I MADS-box TFs in angiosperm evolution remains to be identified. Evolution of angiosperm-specific Type I MADS-box clades is proposed to be linked to the development of the endosperm, a key innovation in angiosperms.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Fisheries
T. A. C. Gordon, H. R. Harding, F. K. Clever, I. K. Davidson, W. Davison, D. W. Montgomery, R. C. Weatherhead, F. M. Windsor, J. D. Armstrong, A. Bardonnet, E. Bergman, J. R. Britton, I. M. Cote, D. D'agostino, L. A. Greenberg, A. R. Harborne, K. K. Kahilainen, N. B. Metcalfe, S. C. Mills, N. J. Milner, F. H. Mittermayer, L. Montorio, S. L. Nedelec, J. M. Prokkola, L. A. Rutterford, A. G. V. Salvanes, S. D. Simpson, A. Vainikka, J. K. Pinnegar, E. M. Santos
JOURNAL OF FISH BIOLOGY
(2018)
Article
Biology
Jenni M. Prokkola, Mikko Nikinmaa
JOURNAL OF EXPERIMENTAL BIOLOGY
(2018)
Article
Biochemistry & Molecular Biology
Kenneth A. Field, Brent J. Sewall, Jenni M. Prokkola, Gregory G. Turner, Marianne F. Gagnon, Thomas M. Lilley, J. Paul White, Joseph S. Johnson, Christopher L. Hauer, DeeAnn M. Reeder
Article
Ecology
Alexandre Lemopoulos, Jenni M. Prokkola, Silva Uusi-Heikkila, Anti Vasemagi, Ari Huusko, Pekka Hyvarinen, Marja-Liisa Koljonen, Jarmo Koskiniemi, Anssi Vainikka
ECOLOGY AND EVOLUTION
(2019)
Review
Physiology
Mikko Nikinmaa, Michael Berenbrink, Colin J. Brauner
Article
Genetics & Heredity
Alexandre Lemopoulos, Silva Uusi-Heikkila, Pekka Hyvarinen, Nico Alioravainen, Jenni M. Prokkola, Chris K. Elvidge, Anti Vasemagi, Anssi Vainikka
G3-GENES GENOMES GENETICS
(2019)
Article
Ecology
Thomas M. Lilley, Jenni M. Prokkola, Anna S. Blomberg, Steve Paterson, Joseph S. Johnson, Gregory G. Turner, Tomas Bartonicka, Erik Bachorec, DeeAnn M. Reeder, Kenneth A. Field
Editorial Material
Physiology
Mikko Nikinmaa
Article
Fisheries
Nico Alioravainen, Jenni M. Prokkola, Alexandre Lemopoulos, Laura Harkonen, Pekka Hyvarinen, Anssi Vainikka
CANADIAN JOURNAL OF FISHERIES AND AQUATIC SCIENCES
(2020)
Article
Ecology
Jenni M. Prokkola, Nico Alioravainen, Lauri Mehtatalo, Pekka Hyvarinen, Alexandre Lemopoulos, Sara Metso, Anssi Vainikka
Summary: The study explores the transgenerational effects of angling on brown trout personality, revealing population-specific impacts on risk taking and exploration tendency, but no effects on standard metabolic rate. Further research is needed to understand the mechanisms underlying the divergent responses between populations.
ECOLOGY AND EVOLUTION
(2021)
Article
Fisheries
Anssi Vainikka, Pekka Hyvarinen, Joni Tiainen, Alexandre Lemopoulos, Nico Alioravainen, Jenni M. Prokkola, Chris K. Elvidge, Robert Arlinghaus
Summary: The study found that adfluvial brown trout's fitness-proxies are affected by predation and natural selection in different fishing environments, with predation mortality being negatively size-dependent and capture probability being positively length- and condition-dependent. Angling behaviors may lead to evolution in behaviors and life histories, offspring of wild fish showed slower growth rates compared to crossbred strains, indicating significant heritable scope for artificial selection on life-history traits.
CANADIAN JOURNAL OF FISHERIES AND AQUATIC SCIENCES
(2021)
Article
Biology
Jenni M. Prokkola, Eirik R. Asheim, Sergey Morozov, Paul Bangura, Jaakko Erkinaro, Annukka Ruokolainen, Craig R. Primmer, Tutku Aykanat
Summary: This study reveals the impact of genetic and phenotypic structure on life-history variation, using Atlantic salmon as an ideal model. The research found the association between early maturation genotype with higher metabolic rates and aerobic scope, as well as the physiological epistasis between late maturation genotypes.
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2022)
Article
Ecology
Eirik R. Asheim, Jenni M. Prokkola, Sergey Morozov, Tutku Aykanat, Craig R. Primmer
Summary: The maturation timing of Atlantic salmon is influenced by the vgll3 gene, but the effect of vgll3 genotype on metabolic rate in juvenile salmon is minimal. This suggests that body condition and maturation are not strongly related to maintenance energy expenditure in this life stage.
ECOLOGY AND EVOLUTION
(2022)
Article
Environmental Sciences
Mirella Kanerva, Mikko Kiljunen, Jyrki Torniainen, Mikko Nikinmaa, Joerg Dutz, Kristiina A. Vuori
SCIENCE OF THE TOTAL ENVIRONMENT
(2020)
Article
Genetics & Heredity
Xiangge Meng, Chengping Li, Yu Hei, Xiang Zhou, Guoli Zhou
Summary: The study used IVT-SAPAS sequencing to analyze the dynamic changes of APA sites during adipogenesis in bovine subcutaneous preadipocytes and intramuscular preadipocytes. The results showed that APA plays an important role in adipocyte differentiation, and UTR-APA switching genes have different trends, with intramuscular preadipocytes tending to use shorter 3'UTR for differentiation. TRIB3, WWTR1, and INSIG1 play important roles in intramuscular preadipocyte differentiation.
Article
Genetics & Heredity
S. Alizadeh, S. Khamse, N. Tajeddin, H. R. Khorram Khorshid, A. Delbari, M. Ohadi
Summary: This study identifies a specific genotype at a CG-rich trinucleotide short tandem repeat (STR) locus that is associated with late-onset neurocognitive disorders such as Alzheimer's disease (AD).
Article
Genetics & Heredity
Shougang Liu, Zhe Zhuang, Fanghua Liu, Xiuqing Yuan, Zeqiao Zhang, Xiaoqian Liang, Xinhui Li, Yongfeng Chen
Summary: This study investigated the effect and mechanism of RPL9 and TIFA in scalp psoriasis, and identified RPL9 as a potential therapeutic target for scalp psoriasis.
Article
Genetics & Heredity
Shiting Wang, Jiaqi Chen, Zhichao Jin, Ying Xing, Ruiping Wang
Summary: This study suggests a causal association between hair color and skin cancers, with light hair colors (red, blonde, and light brown) being associated with an increased risk and dark brown hair being associated with a decreased risk.
Article
Genetics & Heredity
Joseph Hawadak, Loick Pradel Kojom Foko, Rodrigue Roman Dongang Nana, Karmveer Yadav, Veena Pande, Aparup Das, Vineeta Singh
Summary: This study investigates the genetic diversity and natural selection of the Pfama-1 gene in Plasmodium falciparum isolates from Cameroon. The study finds a considerable nucleotide and haplotype diversity, as well as specific mutations in Cameroonian isolates. Positive diversifying selection and the identification of selected codon sites suggest the potential implication of these genetic variations in host immune pressure and parasite-binding complex modulation. The findings provide valuable baseline data for malaria vaccine design.
Article
Genetics & Heredity
Emily Biernat, Mansi Verma, Chhabi K. Govind
Summary: RSC is an essential ATP-dependent chromatin remodeling complex in Saccharomyces cerevisiae. It regulates nucleosome-depleted regions (NDRs) by sliding flanking nucleosomes away from NDRs. Depletion of RSC leads to nucleosome encroachment in NDRs and transcription initiation defects. The study compared the effects of catalytic-dead Sth1 and rapid depletion of Sth1 on transcription. Rapid depletion of Sth1 reduces recruitment of TBP and Pol II, while the catalytic-dead mutant exhibits a severe reduction in TBP binding but accumulates Pol II in coding regions. The results suggest a role for RSC in transcription elongation and termination processes.
Article
Genetics & Heredity
Yunxiao Wei, Yuhan Song, Muhammad Aamir Khan, Chengzhen Liang, Zhigang Meng, Yuan Wang, Sandui Guo, Rui Zhang
Summary: This study analyzed the GhTPP protein family in upland cotton for the first time and identified the important role of GhTPPA_2 in regulating sugar metabolism, improving soluble sugar accumulation, and drought stress tolerance.
Article
Genetics & Heredity
Yannan Geng, Rui Shao, Tiantong Xu, Lilong Zhang
Summary: A novel risk model based on SCUBE3, TNNC1, SPON1, SEPT12 and ULBP1 genes was developed for predicting PMOP risk, with higher risk score indicating higher risk of suffering from PMOP. Significant differences in signaling pathway activities were observed between the high-risk score group and the low-risk score group.
Article
Genetics & Heredity
Randy P. Williams, Corina Lesseur, Haoxiang Cheng, Qian Li, Maya Deyssenroth, Christopher D. Molteno, Ernesta M. Meintjes, Sandra W. Jacobson, Joseph L. Jacobson, Helen Wainwright, Ke Hao, Jia Chen, R. Colin Carter
Summary: The study suggests that heavy alcohol exposure during pregnancy may impact the proportion of fetal placental villi macrophages and increase the expression of inflammatory genes. Further research is needed to explore these effects and evaluate the potential functional roles of placental inflammation in FASD.
Article
Genetics & Heredity
Lvjing Luo, Lishuang Sun, Shu Li, Huiting Liu, Zhengyu Chen, Shi Huang, Yinyin Mo, Genliang Li
Summary: This study analyzed the expression of Ptpn1 and miR-124-3p in testicular tissues of mice and investigated their regulatory relationship. The results showed that Ptpn1 expression was up-regulated in adult mouse testis compared to juvenile mouse testis, while miR-124-3p expression showed an opposite pattern. Further analysis suggested that the down-regulation of miR-124-3p may contribute to the high expression of Ptpn1 in adult mouse testis.
Article
Genetics & Heredity
Gairui Li, Dan Zhao, Xiaolin Peng, Yashuang Zhao
Summary: MiRNA-22 shows potential as a candidate for early diagnosis of colorectal cancer (CRC). The study found higher miR-22 expression levels in the CRC and CRA groups, suggesting its potential as a biomarker for CRC early screening.
Article
Genetics & Heredity
Zhongqiu Zhu, Qianting Yang, Xiaoying Tian, Da Man, Jian Wang, Junfang Zhang, Bingshe Han
Summary: This study constructed a ceRNA network mediated by lncRNAs in cold-acclimated zebrafish ZF4 cells and revealed that upregulation of MSTRG3207 promotes apoptosis by sponging dre-miR-736 during cold acclimation.
Article
Genetics & Heredity
Weitao Chen, Denggao Xiang, Shang Gao, Shuli Zhu, Zhi Wu, Yuefei Li, Jie Li
Summary: Dam construction has negatively impacted the genetic diversity and structure of fish populations. This case study on the endangered Hemibagrus guttatus found low genetic diversity, high levels of inbreeding, and decreasing population size in fragmented populations. Genetic structure and differentiation were also observed, indicating the influence of dams on these fish populations.
Article
Genetics & Heredity
Pooja Singh, Debleena Guin, Bijay Pattnaik, Ritushree Kukreti
Summary: Through systematic literature review and meta-analysis, it was found that idiopathic pulmonary fibrosis is significantly associated with 222 polymorphisms in 118 genes. Four polymorphisms - rs35705950/MUC5B, rs2736100/TERT, rs2076295/DSP, and rs111521887/TOLLIP, exhibited substantial epidemiological evidence supporting their association with IPF risk.
Article
Genetics & Heredity
Jianping Zhang, Zhijun Cai, Fanzhe Feng, Yufeng Peng, Yi Cui, Yongiqing Xu
Summary: This study found that exosomes secreted by young BMSCs can promote the healing of tendon-bone interface after rotator cuff tears. These exosomes can improve extracellular matrix remodeling, osteogenic differentiation, angiogenesis, and stemness of tendon-derived stem cells (TDSCs). The exosomes from young BMSCs have better effects compared to those from aged BMSCs.
