Combined analysis of transposable elements and structural variation in maize genomes reveals genome contraction outpaces expansion
by Manisha Munasinghe, Andrew Read, Michelle C. Stitzer, Baoxing Song, Claire C. Menard, Kristy Yubo Ma, Yaniv Brandvain, Candice N. Hirsch, Nathan Springer
Structural differences between genomes are a major source of genetic variation that contributes to phenotypic differences. Transposable elements, mobile genetic sequences capable of increasing their copy number and propagating themselves within genomes, can generate structural variation. However, their repetitive nature makes it difficult to characterize fine-scale differences in their presence at specific positions, limiting our understanding of their impact on genom...
Source: PLoS Genetics - December 22, 2023 Category: Genetics & Stem Cells Authors: Manisha Munasinghe Source Type: research
NeuroD1-GPX4 signaling leads to ferroptosis resistance in hepatocellular carcinoma
by Ping Huang, Wei Duan, Cao Ruan, Lingxian Wang, Rendy Hosea, Zheng Wu, Jianting Zeng, Shourong Wu, Vivi Kasim
Cell death resistance is a hallmark of tumor cells that drives tumorigenesis and drug resistance. Targeting cell death resistance-related genes to sensitize tumor cells and decrease their cell death threshold has attracted attention as a potential antitumor therapeutic strategy. However, the underlying mechanism is not fully understood. Recent studies have reported that NeuroD1, first discovered as a neurodifferentiation factor, is upregulated in various tumor cells and plays a crucial role in tumorigenesis. How...
Source: PLoS Genetics - December 22, 2023 Category: Genetics & Stem Cells Authors: Ping Huang Source Type: research
The Muscleblind-like protein MBL-1 regulates microRNA expression in < i > Caenorhabditis elegans < /i > through an evolutionarily conserved autoregulatory mechanism
In conclusion, this study provides support for the disruption of cytoplasmic RNA metabolism as a contributor in myotonic dystrophy and paves the way for further exploration of miRNA regulation through MBNL proteins during development and in disease models. (Source: PLoS Genetics)
Source: PLoS Genetics - December 22, 2023 Category: Genetics & Stem Cells Authors: Jens Verbeeren Source Type: research
Autophagic dysfunction and gut microbiota dysbiosis cause chronic immune activation in a < i > Drosophila < /i > model of Gaucher disease
by Magda L. Atilano, Alexander Hull, Catalina-Andreea Romila, Mirjam L. Adams, Jacob Wildfire, Enric Ure ña, Miranda Dyson, Jorge Ivan-Castillo-Quan, Linda Partridge, Kerri J. Kinghorn
Mutations in theGBA1 gene cause the lysosomal storage disorder Gaucher disease (GD) and are the greatest known genetic risk factors for Parkinson ’s disease (PD). Communication between the gut and brain and immune dysregulation are increasingly being implicated in neurodegenerative disorders such as PD. Here, we show that flies lacking theGba1b gene, the main fly orthologue ofGBA1, display widespread NF-kB signalling activation, includin...
Source: PLoS Genetics - December 21, 2023 Category: Genetics & Stem Cells Authors: Magda L. Atilano Source Type: research
Regenerative growth is constrained by < i > brain tumor < /i > to ensure proper patterning in < i > Drosophila < /i >
by Syeda Nayab Fatima Abidi, Felicity Ting-Yu Hsu, Rachel K. Smith-Bolton
Some animals respond to injury by inducing new growth to regenerate the lost structures. This regenerative growth must be carefully controlled and constrained to prevent aberrant growth and to allow correct organization of the regenerating tissue. However, the factors that restrict regenerative growth have not been identified. Using a genetic ablation system in theDrosophila wing imaginal disc, we have identified one mechanism that constrains regenerative growth, impairment of which also leads to erroneous patterning of the final appendage. Regenera...
Source: PLoS Genetics - December 21, 2023 Category: Genetics & Stem Cells Authors: Syeda Nayab Fatima Abidi Source Type: research
Correction: Chromosomal Integrity after UV Irradiation Requires FANCD2-Mediated Repair of Double Strand Breaks
by Mar ía Belén Federico, María Belén Vallerga, Analía Radl, Natalia Soledad Paviolo, José Luis Bocco, Marina Di Giorgio, Gastón Soria, Vanesa Gottifredi (Source: PLoS Genetics)
Source: PLoS Genetics - December 20, 2023 Category: Genetics & Stem Cells Authors: Mar ía Belén Federico Source Type: research
Expression of Concern: < i > EARLY FLOWERING 3 < /i > interactions with < i > PHYTOCHROME B < /i > and < i > PHOTOPERIOD1 < /i > are critical for the photoperiodic regulation of wheat heading time
by The PLOS Genetics Editors (Source: PLoS Genetics)
Source: PLoS Genetics - December 20, 2023 Category: Genetics & Stem Cells Authors: The PLOS Genetics Editors Source Type: research
Expression of Concern: < i > WAPO-A1 < /i > is the causal gene of the 7AL QTL for spikelet number per spike in wheat
by The PLOS Genetics Editors (Source: PLoS Genetics)
Source: PLoS Genetics - December 20, 2023 Category: Genetics & Stem Cells Authors: The PLOS Genetics Editors Source Type: research
Expression of Concern: Epistatic interactions between < i > PHOTOPERIOD1 < /i > , < i > CONSTANS1 < /i > and < i > CONSTANS2 < /i > modulate the photoperiodic response in wheat
by The PLOS Genetics Editors (Source: PLoS Genetics)
Source: PLoS Genetics - December 20, 2023 Category: Genetics & Stem Cells Authors: The PLOS Genetics Editors Source Type: research
Constitutively active CaMKII Drives B lineage acute lymphoblastic leukemia/lymphoma in tp53 mutant zebrafish
by Sarah C. Rothschild, Guanhua Lai, Robert M. Tombes, Wilson K. Clements
Acute lymphoblastic leukemia/lymphoma (ALL) is the most common pediatric cancer and is a malignancy of T or B lineage lymphoblasts. Dysregulation of intracellular Ca2+ levels has been observed in patients with ALL, leading to improper activation of downstream signaling. Here we describe a new zebrafish model of B ALL, generated by expressing human constitutively active CaMKII (CA-CaMKII) intp53 mutant lymphocytes. In this model, B cell hyperplasia in the kidney marrow and spleen progresses to overt leukemia/lymphoma, with only 29% of zebrafish survi...
Source: PLoS Genetics - December 20, 2023 Category: Genetics & Stem Cells Authors: Sarah C. Rothschild Source Type: research
Uncovering associations between pre-existing conditions and COVID-19 Severity: A polygenic risk score approach across three large biobanks
ConclusionBy employing PRS as a proxy for COVID-19 severity, we corroborated known risk factors and identified novel associations between pre-existing clinical phenotypes and COVID-19 severity. Our study highlights the potential value of using PRS when actual outcome data may be limited or inadequate for robust analyses. (Source: PLoS Genetics)
Source: PLoS Genetics - December 19, 2023 Category: Genetics & Stem Cells Authors: Lars G. Fritsche Source Type: research
Molecular traces of < i > Drosophila < /i > hemocytes reveal transcriptomic conservation with vertebrate myeloid cells
by Sang-Ho Yoon, Bumsik Cho, Daewon Lee, Hanji Kim, Jiwon Shim, Jin-Wu NamDrosophila hemocytes serve as the primary defense system against harmful threats, allowing the animals to thrive. Hemocytes are often compared to vertebrate innate immune system cells due to the observed functional similarities between the two. However, the similarities have primarily been established based on a limited number of genes and their functional homologies. Thus, a systematic analysis using transcriptomic data could offer novel insights intoDrosophila hemocyte function and provide new perspectives on the evolution of the immune system. Her...
Source: PLoS Genetics - December 19, 2023 Category: Genetics & Stem Cells Authors: Sang-Ho Yoon Source Type: research
Homeostatic control of stearoyl desaturase expression via patched-like receptor PTR-23 ensures the survival of < i > C < /i > . < i > elegans < /i > during heat stress
This study provides evidence for the negative regulation of fatty acid desaturase expression in the soma ofC.elegans via the non-canonical role of a patched receptor signaling component. Taken together, this constitutes a skin-gut axis for the regulation of lipid desaturation to promote the survival of worms during heat stress. (Source: PLoS Genetics)
Source: PLoS Genetics - December 18, 2023 Category: Genetics & Stem Cells Authors: Siddharth R. Venkatesh Source Type: research
cLD: Rare-variant linkage disequilibrium between genomic regions identifies novel genomic interactions
by Dinghao Wang, Deshan Perera, Jingni He, Chen Cao, Pathum Kossinna, Qing Li, William Zhang, Xingyi Guo, Alexander Platt, Jingjing Wu, Qingrun Zhang
Linkage disequilibrium (LD) is a fundamental concept in genetics; critical for studying genetic associations and molecular evolution. However, LD measurements are only reliable for common genetic variants, leaving low-frequency variants unanalyzed. In this work, we introduce cumulative LD (cLD), a stable statistic that captures the rare-variant LD between genetic regions, which reflects more biological interactions between variants, in addition to lack of recombination. We d...
Source: PLoS Genetics - December 18, 2023 Category: Genetics & Stem Cells Authors: Dinghao Wang Source Type: research
Dual functioning by the PhoR sensor is a key determinant to < i > Mycobacterium tuberculosis < /i > virulence
by Prabhat Ranjan Singh, Harsh Goar, Partha Paul, Khushboo Mehta, Bhanwar Bamniya, Anil Kumar Vijjamarri, Roohi Bansal, Hina Khan, Subramanian Karthikeyan, Dibyendu Sarkar
PhoP-PhoR, one of the 12 two-component systems (TCSs) that empowerM.tuberculosis to sense and adapt to diverse environmental conditions, remains essential for virulence, and therefore, represents a major target to develop novel anti-TB therapies. Although both PhoP and PhoR have been structurally characterized, the signal(s) that this TCS responds to remains unknown. Here, we show that PhoR is a sensor of acidic pH/high salt conditions, which subsequent...
Source: PLoS Genetics - December 15, 2023 Category: Genetics & Stem Cells Authors: Prabhat Ranjan Singh Source Type: research
