Genes, Vol. 12, Pages 748: Ectodermal Dysplasia-Syndactyly Syndrome with Toe-Only Minimal Syndactyly Due to a Novel Mutation in NECTIN4: A Case Report and Literature Review
We report a 5.5-year-old female child affected with EDSS1 due to the novel homozygous frameshift mutation c.1150delC (p.Gln384ArgfsTer7) in the NECTIN4 gene. The patient presents brittle scalp hair, sparse eyebrows and eyelashes, widely spaced conical teeth and dental agenesis, as well as toenail dystrophy and mild PPK. She has minimal proximal syndactyly limited to toes 2–3, which makes the phenotype of our patient peculiar as the overt involvement of both fingers and toes is typical of EDSS1. All previously described mutations are located in the nectin-4 extracellular portion, whereas p.Gln384ArgfsTer7 occurs withi...
Source: Genes - May 17, 2021 Category: Genetics & Stem Cells Authors: Roberta Rotunno Andrea Diociaiuti Maria Lisa Dentici Martina Rinelli Michele Callea Chiara Retrosi Giovanna Zambruno Emanuele Bellacchio May El Hachem Tags: Case Report Source Type: research

Genes, Vol. 12, Pages 750: α-Fodrin in Cytoskeletal Organization and the Activity of Certain Key Microtubule Kinesins
We report that downregulation of α-fodrin in glioblastoma cells, U-251 MG, results in upregulation of genes affecting the regulation of the cytoskeleton, cell cycle and apoptosis. Interestingly, certain key microtubule kinesins such as KIF23, KIF2B and KIF3C are downregulated upon α-fodrin depletion, as validated by real-time PCR studies. (Source: Genes)
Source: Genes - May 17, 2021 Category: Genetics & Stem Cells Authors: Jamuna S. Sreeja Athira Jyothy Suparna Sengupta Tags: Article Source Type: research

Genes, Vol. 12, Pages 751: A Genome-Wide Association Study for Hypertensive Kidney Disease in Korean Men
n Eom Hypertension is one of the major risk factors for chronic kidney disease (CKD), and the coexistence of hypertension and CKD increases morbidity and mortality. Although many genetic factors have been identified separately for hypertension and kidney disease, studies specifically focused on hypertensive kidney disease (HKD) have been rare. Therefore, this study aimed to identify loci or genes associated with HKD. A genome-wide association study (GWAS) was conducted using two Korean cohorts, the Health Examinee (HEXA) and Korean Association REsource (KARE). Consequently, 19 single nucleotide polymorphisms (SNPs) wer...
Source: Genes - May 17, 2021 Category: Genetics & Stem Cells Authors: Hye-Rim Kim Hyun-Seok Jin Yong-Bin Eom Tags: Article Source Type: research

Genes, Vol. 12, Pages 747: Muscat Flavor in Grapevine: A Digital PCR Assay to Track Allelic Variation in VvDXS Gene
ria Terzi The aroma of grapes and derived wines has long been one of the major traits considered in the selection of grapevine varieties through the centuries. In particular, Muscat aromatic grapes have been highly appreciated and widespread since ancient times. Monoterpenes are the key compounds responsible for the Muscat flavor. A major QTL affecting monoterpene level has been found to co-localize with the 1-deoxy-D-xylulose 5-phosphate synthase (VvDXS) gene, encoding for the 1-deoxy-D-xylulose 5-phosphate synthase enzyme involved in the plastidial pathway of terpene biosynthesis. In more detail, a single nucleotide ...
Source: Genes - May 16, 2021 Category: Genetics & Stem Cells Authors: Caterina Morcia Giorgio Tumino Stefano Raimondi Anna Schneider Valeria Terzi Tags: Communication Source Type: research

Genes, Vol. 12, Pages 749: Molecular Pathways Associated with Kallikrein 6 Overexpression in Colorectal Cancer
A. Ignatenko Colorectal cancer (CRC) remains one of the leading causes of cancer-related death worldwide. The high mortality of CRC is related to its ability to metastasize to distant organs. The kallikrein-related peptidase Kallikrein 6 (KLK6) is overexpressed in CRC and contributes to cancer cell invasion and metastasis. The goal of this study was to identify KLK6-associated markers for the CRC prognosis and treatment. Tumor Samples from the CRC patients with significantly elevated KLK6 transcript levels were identified in the RNA-Seq data from Cancer Genome Atlas (TCGA) and their expression profiles were evaluated ...
Source: Genes - May 16, 2021 Category: Genetics & Stem Cells Authors: Ritu Pandey Muhan Zhou Yuliang Chen Dalila Darmoul Conner C. Kisiel Valentine N. Nfonsam Natalia A. Ignatenko Tags: Article Source Type: research

Genes, Vol. 12, Pages 746: The Seed Development Factors TT2 and MYB5 Regulate Heat Stress Response in Arabidopsis
ert Hirt Abdelhafid Bendahmane HEAT SHOCK FACTOR A2 (HSFA2) is a regulator of multiple environmental stress responses required for stress acclimation. We analyzed HSFA2 co-regulated genes and identified 43 genes strongly co-regulated with HSFA2 during multiple stresses. Motif enrichment analysis revealed an over-representation of the site II element (SIIE) in the promoters of these genes. In a yeast 1-hybrid screen with the SIIE, we identified the closely related R2R3-MYB transcription factors TT2 and MYB5. We found overexpression of MYB5 or TT2 rendered plants heat stress tolerant. In contrast, tt2, myb5, and tt2/my...
Source: Genes - May 15, 2021 Category: Genetics & Stem Cells Authors: Pierre Jacob Gwilherm Brisou Marion Dalmais Johanne Th évenin Froukje van der Wal David Latrasse Ravi Suresh Devani Moussa Benhamed Bertrand Dubreucq Adnane Boualem Loic Lepiniec Richard G. H. Immink Heribert Hirt Abdelhafid Bendahmane Tags: Article Source Type: research

Genes, Vol. 12, Pages 741: Making Sense of a Health Threat: Illness Representations, Coping, and Psychological Distress among BRCA1/2 Mutation Carriers
In this study, we investigated associations between illness representations, coping strategies and psychological distress. N = 101 BRCA1/2 mutation carriers answered self-report questionnaires on illness representations, coping strategies, cancer worry and depressive symptoms. Women without cancer were compared to women with a previous cancer diagnosis. Illness representations explained 50% and 45% of the variability in cancer worry and depressive symptoms, respectively. Woman perceiving severe consequences (β = 0.29, p < 0.01) and having more concerns (β = 0.37, p < 0.01) were found to repo...
Source: Genes - May 14, 2021 Category: Genetics & Stem Cells Authors: Hannah Brand Dorothee Speiser Laura Besch Julia Roseman Friederike Kendel Tags: Article Source Type: research

Genes, Vol. 12, Pages 742: MET Expression and Cancer Stem Cell Networks Impact Outcome in High-Grade Serous Ovarian Cancer
bäck Gabriella Honeth Ingrid Hedenfalk Overexpression of the receptor tyrosine kinase MET has been linked to poor survival in several cancer types, and MET has been suggested to interact with stem cell networks. In vitro studies have further suggested a possible benefit of a combined treatment using PARP and MET inhibitors. We used a tissue microarray (TMA) with 130 samples of advanced-stage high-grade serous fallopian tube/ovarian cancer (HGSC) to investigate the prognostic value of MET protein expression alone and in combination with the stem cell factor SOX2. The possible synergistic effects of a PARP and M...
Source: Genes - May 14, 2021 Category: Genetics & Stem Cells Authors: Maria B ååth Jenny-Maria J önsson Sofia Westbom Fremer Laura Mart ín de la Fuente Lena Tran Susanne Malander P äivi Kannisto Anna M åsbäck Gabriella Honeth Ingrid Hedenfalk Tags: Article Source Type: research

Genes, Vol. 12, Pages 743: Pilot Screening of Cell-Free mtDNA in NIPT: Quality Control, Variant Calling, and Haplogroup Determination
In this study, we analyse mtDNA pool from 645 cell-free DNA (cfDNA) samples of pregnant women from different regions of Russia, explore the effects of transportation and storing conditions on mtDNA content, analyse effects, frequency and location of mitochondrial variants called from samples and perform haplogroup analysis, revealing the most common mitochondrial superclades. We have shown that, despite the relatively low sequencing depth of unamplified mtDNA from cfDNA samples, the mtDNA analysis in these samples is still an informative instrument suitable for research and screening purposes. (Source: Genes)
Source: Genes - May 14, 2021 Category: Genetics & Stem Cells Authors: Alisa Morshneva Polina Kozyulina Elena Vashukova Olga Tarasenko Natalia Dvoynova Anastasia Chentsova Olga Talantova Alexander Koroteev Dmitrii Ivanov Elena Serebryakova Tatyana Ivashchenko Aitalina Sukhomyasova Nadezhda Maksimova Olesya Bespalova Igor Kog Tags: Article Source Type: research

Genes, Vol. 12, Pages 744: Whole-Exome Sequencing, Proteome Landscape, and Immune Cell Migration Patterns in a Clinical Context of Menkes Disease
We describe the case of a male patient of 8 months of age with silvery hair, tan skin color, hypotonia, alterations in neurodevelopment, presence of seizures, and low values of plasma ceruloplasmin. Trio-whole-exome sequencing (Trio-WES) analysis, plasma proteome screening, and blood cell migration assays were carried out. Trio-WES revealed a hemizygous change c.4190C > T (p.S1397F) in exon 22 of the ATP7A gene. Compared with his parents and with child controls, 11 plasma proteins were upregulated and 59 downregulated in the patient. According to their biological processes, 42 (71.2%) of downregulated proteins h...
Source: Genes - May 14, 2021 Category: Genetics & Stem Cells Authors: Margarita L. Martinez-Fierro Griselda A. Cabral-Pacheco Idalia Garza-Veloz Jesus Acu ña-Quiñones Laura E. Martinez-de-Villarreal Marisol Ibarra-Ramirez Joke Beuten Samantha E. Sanchez-Guerrero Laura Villarreal-Martinez Ivan Delgado-Enciso Iram P. Rodrig Tags: Article Source Type: research

Genes, Vol. 12, Pages 745: Novel QTL Associated with Shoot Branching Identified in Doubled Haploid Rice (Oryza sativa L.) under Low Nitrogen Cultivation
n Ko Jong-Hee Lee Shoot branching is considered as an important trait for the architecture of plants and contributes to their growth and productivity. In cereal crops, such as rice, shoot branching is controlled by many factors, including phytohormones signaling networks, operating either in synergy or antagonizing each other. In rice, shoot branching indicates the ability to produce more tillers that are essential for achieving high productivity and yield potential. In the present study, we evaluated the growth and development, and yield components of a doubled haploid population derived from a cross between 93-11 (...
Source: Genes - May 14, 2021 Category: Genetics & Stem Cells Authors: Youngho Kwon Nkulu Rolly Kabange Ji-Yun Lee So-Myeong Lee Jin-Kyung Cha Dongjin Shin Jun-Hyeon Cho Ju-Won Kang Jong-Min Ko Jong-Hee Lee Tags: Article Source Type: research

Genes, Vol. 12, Pages 739: Alternative Strategies for Multi-Stress Tolerance and Yield Improvement in Millets
Osena Millets are important cereal crops cultivated in arid and semiarid regions of the world, particularly Africa and southeast Asia. Climate change has triggered multiple abiotic stresses in plants that are the main causes of crop loss worldwide, reducing average yield for most crops by more than 50%. Although millets are tolerant to most abiotic stresses including drought and high temperatures, further improvement is needed to make them more resilient to unprecedented effects of climate change and associated environmental stresses. Incorporation of stress tolerance traits in millets will improve their productivity i...
Source: Genes - May 14, 2021 Category: Genetics & Stem Cells Authors: Muhammad Numan Desalegn D. Serba Ayalew Ligaba-Osena Tags: Review Source Type: research

Genes, Vol. 12, Pages 740: Evolution of Reproductive Life History in Mammals and the Associated Change of Functional Constraints
shino Phylogenetic trees based on multiple genomic loci enable us to estimate the evolution of functional constraints that operate on genes based on lineage-specific fluctuation of the evolutionary rate at particular gene loci, “gene–branch interactions”. Using this information as predictors, our previous work inferred that the common ancestor of placental mammals was nocturnal, insectivorous, solitary, and bred seasonally. Here, we added seven new continuous traits including lifespan, bodyweight, and five reproduction-related traits and inferred the coevolution network of 14 core life history traits ...
Source: Genes - May 14, 2021 Category: Genetics & Stem Cells Authors: Jiaqi Wu Takahiro Yonezawa Hirohisa Kishino Tags: Article Source Type: research

Genes, Vol. 12, Pages 724: Generation of Iron-Independent Siderophore-Producing Agaricus bisporus through the Constitutive Expression of hapX
Ro Agaricus bisporus secretes siderophore to uptake environmental iron. Siderophore secretion in A. bisporus was enabled only in the iron-free minimal medium due to iron repression of hapX, a transcriptional activator of siderophore biosynthetic genes. Aiming to produce siderophore using conventional iron-containing complex media, we constructed a recombinant strain of A. bisporus that escapes hapX gene repression. For this, the A. bisporushapX gene was inserted next to the glyceraldehyde 3-phosphate dehydrogenase promoter (pGPD) in a binary vector, pBGgHg, for the constitutive expression of hapX. Transformants of A. ...
Source: Genes - May 13, 2021 Category: Genetics & Stem Cells Authors: Min-Seek Kim Hyeon-Su Ro Tags: Article Source Type: research

Genes, Vol. 12, Pages 725: Editorial: “Evolutionary Genetics of Insect Innate Immunity”
Genes, Vol. 12, Pages 725: Editorial: “Evolutionary Genetics of Insect Innate Immunity” Genes doi: 10.3390/genes12050725 Authors: Ioannis Eleftherianos The insect innate immune system is under strong selection pressure to evolve resistance to pathogenic infections [...] (Source: Genes)
Source: Genes - May 13, 2021 Category: Genetics & Stem Cells Authors: Ioannis Eleftherianos Tags: Editorial Source Type: research

Genes, Vol. 12, Pages 726: Craniofacial Diseases Caused by Defects in Intracellular Trafficking
Kim Cells use membrane-bound carriers to transport cargo molecules like membrane proteins and soluble proteins, to their destinations. Many signaling receptors and ligands are synthesized in the endoplasmic reticulum and are transported to their destinations through intracellular trafficking pathways. Some of the signaling molecules play a critical role in craniofacial morphogenesis. Not surprisingly, variants in the genes encoding intracellular trafficking machinery can cause craniofacial diseases. Despite the fundamental importance of the trafficking pathways in craniofacial morphogenesis, relatively less emphasis is...
Source: Genes - May 13, 2021 Category: Genetics & Stem Cells Authors: Chung-Ling Lu Jinoh Kim Tags: Review Source Type: research

Genes, Vol. 12, Pages 727: The ATM Gene in Breast Cancer: Its Relevance in Clinical Practice
ta Camillo Porta Molecular alterations of the Ataxia-telangiectasia (AT) gene are frequently detected in breast cancer (BC), with an incidence ranging up to 40%. The mutated form, the Ataxia-telangiectasia mutated (ATM) gene, is involved in cell cycle control, apoptosis, oxidative stress, and telomere maintenance, and its role as a risk factor for cancer development is well established. Recent studies have confirmed that some variants of ATM are associated with an increased risk of BC development and a worse prognosis. Thus, many patients harboring ATM mutations develop intermediate- and high-grade disease, and there...
Source: Genes - May 13, 2021 Category: Genetics & Stem Cells Authors: Luigia Stefania Stucci Valeria Intern ò Marco Tucci Martina Perrone Francesco Mannavola Raffaele Palmirotta Camillo Porta Tags: Review Source Type: research

Genes, Vol. 12, Pages 728: MTOR Signaling and Metabolism in Early T Cell Development
cinto The mechanistic target of rapamycin (mTOR) controls cell fate and responses via its functions in regulating metabolism. Its role in controlling immunity was unraveled by early studies on the immunosuppressive properties of rapamycin. Recent studies have provided insights on how metabolic reprogramming and mTOR signaling impact peripheral T cell activation and fate. The contribution of mTOR and metabolism during early T-cell development in the thymus is also emerging and is the subject of this review. Two major T lineages with distinct immune functions and peripheral homing organs diverge during early thymic devel...
Source: Genes - May 13, 2021 Category: Genetics & Stem Cells Authors: Guy Werlen Ritika Jain Estela Jacinto Tags: Review Source Type: research

Genes, Vol. 12, Pages 729: The Genotoxic and Pro-Apoptotic Activities of Advanced Glycation End-Products (MAGE) Measured with Micronuclei Assay Are Inhibited by Their Low Molecular Mass Counterparts
We examined the genotoxic activity of new products synthesized under nonaqueous conditions. These were high molecular mass MAGEs (HMW–MAGEs) formed from protein and melibiose and low molecular mass MAGEs (LMW–MAGEs) obtained from the melibiose and N-α-acetyllysine and N-α-acetylarginine. We have observed by measuring of micronuclei in human lymphocytes in vitro that the studied HMW–MAGEs expressed the genotoxicity. The number of micronuclei (MN) in lymphocytes reached 40.22 ± 5.34 promille (MN/1000CBL), compared to 28.80 ± 6.50 MN/1000 CBL for the reference BSA–MG, whereas ...
Source: Genes - May 13, 2021 Category: Genetics & Stem Cells Authors: Monika Czech Maria Konopacka Jacek Rogoli ński Zbigniew Maniakowski Magdalena Staniszewska Łukasz Łaczmański Danuta Witkowska Andrzej Gamian Tags: Article Source Type: research

Genes, Vol. 12, Pages 730: Can Knowledge of Genetic Distances, Genome Sizes and Chromosome Numbers Support Breeding Programs in Hardy Geraniums?
Emmy Dhooghe Breeding programs in ornamentals can be facilitated by integrating knowledge of phylogenetic relatedness of potential parents along with other genomic information. Using AFLP, genetic distances were determined for 59 Geranium genotypes, comprising 55 commercial cultivars of the three subgenera of a total collection of 61 Geranium genotypes. A subgroup of 45 genotypes, including intragroup and intergroup hybrids, were selected and further characterized for genome sizes and chromosome numbers. The variation in genome size ranged from 1.51 ± 0.01 pg/2C to 12.94 ± 0.07 pg/2C. The chromosome numb...
Source: Genes - May 13, 2021 Category: Genetics & Stem Cells Authors: Mehrdad Akbarzadeh Katrijn Van Laere Leen Leus Jan De Riek Johan Van Huylenbroeck Stefaan P.O. Werbrouck Emmy Dhooghe Tags: Article Source Type: research

Genes, Vol. 12, Pages 733: Analysis of Skin Pigmentation and Genetic Ancestry in Three Subpopulations from Pakistan: Punjabi, Pashtun, and Baloch
Børsting Skin pigmentation is one of the most prominent and variable phenotypes in humans. We compared the alleles of 163 SNPs and indels from the Human Pigmentation (HuPi) AmpliSeq™ Custom panel, and biogeographic ancestry with the quantitative skin pigmentation levels on the upper arm, lower arm, and forehead of 299 Pakistani individuals from three subpopulations: Baloch, Pashtun, and Punjabi. The biogeographic ancestry of each individual was estimated using the Precision ID Ancestry Panel. All individuals were mainly of mixed South-Central Asian and European ancestry. However, the Baloch individuals al...
Source: Genes - May 13, 2021 Category: Genetics & Stem Cells Authors: Muhammad Adnan Shan Olivia Strunge Meyer Mie Refn Niels Morling Jeppe Dyrberg Andersen Claus B ørsting Tags: Article Source Type: research

Genes, Vol. 12, Pages 731: Modifier Genes in Microcephaly: A Report on WDR62, CEP63, RAD50 and PCNT Variants Exacerbating Disease Caused by Biallelic Mutations of ASPM and CENPJ
an Muhammad Jameel Sheraz Khan Muhammad Tariq Iram Anjum Janine Altmüller Holger Thiele Stefan Höning Shahid Mahmood Baig Peter Nürnberg Muhammad Sajid Hussain Congenital microcephaly is the clinical presentation of significantly reduced head circumference at birth. It manifests as both non-syndromic—microcephaly primary hereditary (MCPH)—and syndromic forms and shows considerable inter- and intrafamilial variability. It has been hypothesized that additional genetic variants may be responsible for this variability, but data are sparse. We have conducted deep phenotyping an...
Source: Genes - May 13, 2021 Category: Genetics & Stem Cells Authors: Ehtisham Ul Haq Makhdoom Syeda Seema Waseem Maria Iqbal Uzma Abdullah Ghulam Hussain Maria Asif Birgit Budde Wolfgang H öhne Sigrid Tinschert Saadia Maryam Saadi Hammad Yousaf Zafar Ali Ambrin Fatima Emrah Kaygusuz Ayaz Khan Muhammad Jameel Sheraz Khan M Tags: Article Source Type: research

Genes, Vol. 12, Pages 734: The Molecular Basis of Calcium and Phosphorus Inherited Metabolic Disorders
aliou Calcium (Ca) and Phosphorus (P) hold a leading part in many skeletal and extra-skeletal biological processes. Their tight normal range in serum mirrors their critical role in human well-being. The signalling “voyage” starts at Calcium Sensing Receptor (CaSR) localized on the surface of the parathyroid glands, which captures the “oscillations” of extracellular ionized Ca and transfers the signal downstream. Parathyroid hormone (PTH), Vitamin D, Fibroblast Growth Factor (FGF23) and other receptors or ion-transporters, work synergistically and establish a highly regulated signalling circuit b...
Source: Genes - May 13, 2021 Category: Genetics & Stem Cells Authors: Anna Papadopoulou Evangelia Bountouvi Fotini-Eleni Karachaliou Tags: Review Source Type: research

Genes, Vol. 12, Pages 735: Mapping of Quantitative Trait Loci Controlling Egg-Quality and -Production Traits in Japanese Quail (Coturnix japonica) Using Restriction-Site Associated DNA Sequencing
Masaoki Tsudzuki This research was conducted to identify quantitative trait loci (QTL) associated with egg-related traits by constructing a genetic linkage map based on single nucleotide polymorphism (SNP) markers using restriction-site associated DNA sequencing (RAD-seq) in Japanese quail. A total of 138 F2 females were produced by full-sib mating of F1 birds derived from an intercross between a male of the large-sized strain with three females of the normal-sized strain. Eggs were investigated at two different stages: the beginning stage of egg-laying and at 12 weeks of age (second stage). Five eggs were analyzed fo...
Source: Genes - May 13, 2021 Category: Genetics & Stem Cells Authors: Mohammad Ibrahim Haqani Shigeru Nomura Michiharu Nakano Tatsuhiko Goto Atsushi J. Nagano Atsushi Takenouchi Yoshiaki Nakamura Akira Ishikawa Masaoki Tsudzuki Tags: Article Source Type: research

Genes, Vol. 12, Pages 736: Statistical Learning Methods Applicable to Genome-Wide Association Studies on Unbalanced Case-Control Disease Data
Zeng Despite the fact that imbalance between case and control groups is prevalent in genome-wide association studies (GWAS), it is often overlooked. This imbalance is getting more significant and urgent as the rapid growth of biobanks and electronic health records have enabled the collection of thousands of phenotypes from large cohorts, in particular for diseases with low prevalence. The unbalanced binary traits pose serious challenges to traditional statistical methods in terms of both genomic selection and disease prediction. For example, the well-established linear mixed models (LMM) yield inflated type I erro...
Source: Genes - May 13, 2021 Category: Genetics & Stem Cells Authors: Dai Fu Zhao Zeng Tags: Review Source Type: research

Genes, Vol. 12, Pages 737: Exploration of Alternative Splicing Events in Mesenchymal Stem Cells from Human Induced Pluripotent Stem Cells
This study provides valuable insight into the biology of iMSCs and the translation of mechanistic understanding of iMSCs into therapeutic applications. (Source: Genes)
Source: Genes - May 13, 2021 Category: Genetics & Stem Cells Authors: Ji-Eun Jeong Binna Seol Han-Seop Kim Jae-Yun Kim Yee-Sook Cho Tags: Article Source Type: research

Genes, Vol. 12, Pages 732: Identification and Validation of Reference Genes for Gene Expression Analysis in Schima superba
In this study, 19 candidate reference genes were selected and evaluated for their expression stability in different tissues of S. superba. Three software programs (geNorm, NormFinder, and BestKeeper) were used to evaluate the reference gene transcript stabilities, and comprehensive stability ranking was generated by the geometric mean method. Our results show that SsuACT was the most stable reference gene and that SsuACT + SsuRIB was the best reference gene combination for different tissues. Finally, the stable and less stable reference genes were verified using SsuSND1 expression in different tissues. To our knowledge, th...
Source: Genes - May 13, 2021 Category: Genetics & Stem Cells Authors: Zhongyi Yang Rui Zhang Zhichun Zhou Tags: Article Source Type: research

Genes, Vol. 12, Pages 738: Schuurs –Hoeijmakers Syndrome (PACS1 Neurodevelopmental Disorder): Seven Novel Patients and a Review
Genes, Vol. 12, Pages 738: Schuurs–Hoeijmakers Syndrome (PACS1 Neurodevelopmental Disorder): Seven Novel Patients and a Review Genes doi: 10.3390/genes12050738 Authors: Jair Tenorio-Castaño Beatriz Morte Julián Nevado Víctor Martinez-Glez Fernando Santos-Simarro Sixto García-Miñaúr María Palomares-Bralo Marta Pacio-Míguez Beatriz Gómez Pedro Arias Alba Alcochea Juan Carrión Patricia Arias Berta Almoguera Fermina López-Grondona Isabel Lorda Enrique Galán-Gómez Irene Valenzuela María...
Source: Genes - May 13, 2021 Category: Genetics & Stem Cells Authors: Jair Tenorio-Casta ño Beatriz Morte Juli án Nevado V íctor Martinez-Glez Fernando Santos-Simarro Sixto Garc ía-Miñaúr Mar ía Palomares-Bralo Marta Pacio-M íguez Beatriz G ómez Pedro Arias Alba Alcochea Juan Carri ón Patricia Arias Berta Almoguer Tags: Article Source Type: research

Genes, Vol. 12, Pages 721: The Adenine/Thymine Deleterious Selection Model for GC Content Evolution at the Third Codon Position of the Histone Genes in Drosophila
o The evolution of the GC (guanine cytosine) content at the third codon position of the histone genes (H1, H2A, H2B, H3, H4, H2AvD, H3.3A, H3.3B, and H4r) in 12 or more Drosophila species is reviewed. For explaining the evolution of the GC content at the third codon position of the genes, a model assuming selection with a deleterious effect for adenine/thymine and a size effect is presented. The applicability of the model to whole-genome genes is also discussed. (Source: Genes)
Source: Genes - May 12, 2021 Category: Genetics & Stem Cells Authors: Yoshinori Matsuo Tags: Review Source Type: research

Genes, Vol. 12, Pages 722: Making Sense of Genetic Information: The Promising Evolution of Clinical Stratification and Precision Oncology Using Machine Learning
en Kaneko Precision medicine is a medical approach to administer patients with a tailored dose of treatment by taking into consideration a person’s variability in genes, environment, and lifestyles. The accumulation of omics big sequence data led to the development of various genetic databases on which clinical stratification of high-risk populations may be conducted. In addition, because cancers are generally caused by tumor-specific mutations, large-scale systematic identification of single nucleotide polymorphisms (SNPs) in various tumors has propelled significant progress of tailored treatments of tumors (i.e...
Source: Genes - May 12, 2021 Category: Genetics & Stem Cells Authors: Mahaly Baptiste Sarah Shireen Moinuddeen Courtney Lace Soliz Hashimul Ehsan Gen Kaneko Tags: Review Source Type: research

Genes, Vol. 12, Pages 720: Mitochondrial D-Loop Region Methylation and Copy Number in Peripheral Blood DNA of Parkinson ’s Disease Patients
Genes, Vol. 12, Pages 720: Mitochondrial D-Loop Region Methylation and Copy Number in Peripheral Blood DNA of Parkinson’s Disease Patients Genes doi: 10.3390/genes12050720 Authors: Andrea Stoccoro Adam R. Smith Filippo Baldacci Claudia Del Gamba Annalisa Lo Gerfo Roberto Ceravolo Katie Lunnon Lucia Migliore Fabio Coppedè Altered mitochondrial DNA (mtDNA) methylation has been detected in several human pathologies, although little attention has been given to neurodegenerative diseases. Recently, altered methylation levels of the mitochondrial displacement loop (D-loop) region, which regul...
Source: Genes - May 12, 2021 Category: Genetics & Stem Cells Authors: Andrea Stoccoro Adam R. Smith Filippo Baldacci Claudia Del Gamba Annalisa Lo Gerfo Roberto Ceravolo Katie Lunnon Lucia Migliore Fabio Copped è Tags: Article Source Type: research

Genes, Vol. 12, Pages 723: New Insights into the Therapeutic Applications of CRISPR/Cas9 Genome Editing in Breast Cancer
Harati Breast cancer is one of the most prevalent forms of cancer globally and is among the leading causes of death in women. Its heterogenic nature is a result of the involvement of numerous aberrant genes that contribute to the multi-step pathway of tumorigenesis. Despite the fact that several disease-causing mutations have been identified, therapy is often aimed at alleviating symptoms rather than rectifying the mutation in the DNA sequence. The Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/Cas9 is a groundbreaking tool that is being utilized for the identification and validation of genomic tar...
Source: Genes - May 12, 2021 Category: Genetics & Stem Cells Authors: Munazza Ahmed Grace Hope Daoud Asmaa Mohamed Rania Harati Tags: Review Source Type: research

Genes, Vol. 12, Pages 718: Genome-Wide Association Study Identified Novel Candidate Loci/Genes Affecting Lodging Resistance in Rice
u Xingfei Zheng Lodging reduces rice yield, but increasing lodging resistance (LR) usually limits yield potential. Stem strength and leaf type are major traits related to LR and yield, respectively. Hence, understanding the genetic basis of stem strength and leaf type is of help to reduce lodging and increase yield in LR breeding. Here, we carried out an association analysis to identify quantitative trait locus (QTLs) affecting stem strength-related traits (internode length/IL, stem wall thickness/SWT, stem outer diameter/SOD, and stem inner diameter/SID) and leaf type-associated traits (Flag leaf length/FLL, Flag le...
Source: Genes - May 11, 2021 Category: Genetics & Stem Cells Authors: Bingxin Meng Tao Wang Yi Luo Deze Xu Lanzhi Li Ying Diao Zhiyong Gao Zhongli Hu Xingfei Zheng Tags: Article Source Type: research

Genes, Vol. 12, Pages 719: Discovery and Characterization of a Novel Tomato mlo Mutant from an EMS Mutagenized Micro-Tom Population
In this study, we have developed a new genetic resource (M200) in the tomato cv. Micro-Tom genetic background by means of ethyl methane sulfonate (EMS) mutagenesis. The mutant M200 containing a novel allele (the m200 allele) of the tomato SlMLO1 gene showed profound resistance against powdery mildew with no fungal sporulation. Compared to the coding sequence of the SlMLO1 gene, the m200 allele carries a point mutation at T65A. The SNP results in a premature stop codon L22* located in the first transmembrane domain of the complete SlMLO1 protein. The length of the predicted protein is 21 amino acids, while the SlMLO1 full-l...
Source: Genes - May 11, 2021 Category: Genetics & Stem Cells Authors: Zhe Yan Michela Appiano Ageeth van Tuinen Fien Meijer-Dekens Danny Schipper Dongli Gao Robin Huibers Richard G. F. Visser Yuling Bai Anne-Marie A. Wolters Tags: Article Source Type: research

Genes, Vol. 12, Pages 714: SLC26A2-Associated Diastrophic Dysplasia and rMED —Clinical Features in Affected Finnish Children and Review of the Literature
Genes, Vol. 12, Pages 714: SLC26A2-Associated Diastrophic Dysplasia and rMED—Clinical Features in Affected Finnish Children and Review of the Literature Genes doi: 10.3390/genes12050714 Authors: Helmi Härkönen Petra Loid Outi Mäkitie Diastrophic dysplasia (DTD) is a rare osteochondrodysplasia characterized by short-limbed short stature and joint dysplasia. DTD is caused by mutations in SLC26A2 and is particularly common in the Finnish population. However, the disease incidence in Finland and clinical features in affected individuals have not been recently explored. This registry-based study...
Source: Genes - May 11, 2021 Category: Genetics & Stem Cells Authors: Helmi H ärkönen Petra Loid Outi M äkitie Tags: Article Source Type: research

Genes, Vol. 12, Pages 715: Association between the FTO A/T Polymorphism and Elite Athlete Status in Caucasian Swimmers
ec The FTO A/T polymorphism (rs9939609) has been strongly associated with body mass-related traits in nonathletic populations, but rarely with elite athletic performance. The aim of the study was to investigate the association between the A/T polymorphism and athlete status in elite swimmers. Polish swimmers (n = 196) who competed in national and international competition at short- (SDS; 50–200 m; n = 147) and long-distance events (LDS; ≥400 m; n = 49) were recruited. The control group included 379 unrelated, sedentary young participants. The participants were all Caucasians. Genotyping was carried out using r...
Source: Genes - May 11, 2021 Category: Genetics & Stem Cells Authors: Piotr Zmijewski Agata Leo ńska-Duniec Tags: Article Source Type: research

Genes, Vol. 12, Pages 716: A Novel Phenotype of Junctional Epidermolysis Bullosa with Transient Skin Fragility and Predominant Ocular Involvement Responsive to Human Amniotic Membrane Eyedrops
We report a novel JEB phenotype distinguished by the complete resolution of skin fragility in infancy and persistent ocular involvement with unremitting and painful corneal abrasions. Biallelic LAMB3 mutations c.3052-5C>G and c.3492_3493delCG were identified as the molecular basis for this phenotype, with one mutation being a hypomorphic splice variant that allows residual wild-type laminin-332 production. The reduced laminin-332 level was associated with impaired keratinocyte adhesion. Then, we also investigated the therapeutic power of a human amniotic membrane (AM) eyedrop preparation for corneal lesions. AM ...
Source: Genes - May 11, 2021 Category: Genetics & Stem Cells Authors: Daniele Castiglia Paola Fortugno Angelo Giuseppe Condorelli Sabina Barresi Naomi De Luca Simone Pizzi Iria Neri Claudio Graziano Diletta Trojan Diego Ponzin Sabrina Rossi Giovanna Zambruno Marco Tartaglia Tags: Article Source Type: research

Genes, Vol. 12, Pages 717: UbiComb: A Hybrid Deep Learning Model for Predicting Plant-Specific Protein Ubiquitylation Sites
In this study, we proposed a novel approach for predicting plant ubiquitylation sites using a hybrid deep learning model by utilizing convolutional neural network and long short-term memory. The proposed method uses the actual protein sequence and physicochemical properties as inputs to the model and provides more robust predictions. The proposed predictor achieved the best result with accuracy values of 80% and 81% and F-scores of 79% and 82% on the 10-fold cross-validation and an independent dataset, respectively. Moreover, we also compared the testing of the independent dataset with popular ubiquitylation predictors; th...
Source: Genes - May 11, 2021 Category: Genetics & Stem Cells Authors: Arslan Siraj Dae Yeong Lim Hilal Tayara Kil To Chong Tags: Article Source Type: research

Genes, Vol. 12, Pages 708: Genetic and Genome-Wide Association Analysis of Yearling Weight Gain in Israel Holstein Dairy Calves
Ezra Yearling weight gain in male and female Israeli Holstein calves, defined as 365 × ((weight − 35)/age at weight) + 35, was analyzed from 814,729 records on 368,255 animals from 740 herds recorded between 1994 and 2021. The variance components were calculated based on valid records from 2008 through 2017 for each sex separately and both sexes jointly by a single-trait individual animal model analysis, which accounted for repeat records on animals. The analysis model also included the square root, linear, and quadratic effects of age at weight. Heritability and repeatability were 0.35 and 0.71 in the ana...
Source: Genes - May 10, 2021 Category: Genetics & Stem Cells Authors: Moran Gershoni Joel Ira Weller Ephraim Ezra Tags: Article Source Type: research

Genes, Vol. 12, Pages 709: Rooting in the Desert: A Developmental Overview on Desert Plants
lilou Plants, as sessile organisms, have evolved a remarkable developmental plasticity to cope with their changing environment. When growing in hostile desert conditions, plants have to grow and thrive in heat and drought. This review discusses how desert plants have adapted their root system architecture (RSA) to cope with scarce water availability and poor nutrient availability in the desert soil. First, we describe how some species can survive by developing deep tap roots to access the groundwater while others produce shallow roots to exploit the short rain seasons and unpredictable rainfalls. Then, we discuss how d...
Source: Genes - May 10, 2021 Category: Genetics & Stem Cells Authors: Gwendolyn K. Kirschner Ting Ting Xiao Ikram Blilou Tags: Review Source Type: research

Genes, Vol. 12, Pages 710: Novel Homozygous Inactivating Mutation in the PCSK1 Gene in an Infant with Congenital Malabsorptive Diarrhea
olina John W. Creemers Proprotein convertase 1/3 (PC1/3), encoded by the PCSK1 gene, is expressed in neuronal and (entero)endocrine cell types, where it cleaves and hence activates a number of protein precursors that play a key role in energy homeostasis. Loss-of-function mutations in PCSK1 cause a recessive complex endocrinopathy characterized by malabsorptive diarrhea and early-onset obesity. Despite the fact that neonatal malabsorptive diarrhea is observed in all patients, it has remained understudied. The aim of this study was to investigate the enteroendocrine pathologies in a male patient with congenital PCSK1 ...
Source: Genes - May 10, 2021 Category: Genetics & Stem Cells Authors: Laetitia Aerts Nathalie A. Terry Nina N. Sainath Clarivet Torres Mart ín G. Martín Bruno Ramos-Molina John W. Creemers Tags: Article Source Type: research

Genes, Vol. 12, Pages 711: Endopolyploidy Variation in Wild Barley Seeds across Environmental Gradients in Israel
Ales Pecinka Wild barley is abundant, occupying large diversity of sites, ranging from the northern mesic Mediterranean meadows to the southern xeric deserts in Israel. This is also reflected in its wide phenotypic heterogeneity. We investigated the dynamics of DNA content changes in seed tissues in ten wild barley accessions that originated from an environmental gradient in Israel. The flow cytometric measurements were done from the time shortly after pollination up to the dry seeds. We show variation in mitotic cell cycle and endoreduplication dynamics in both diploid seed tissues (represented by seed maternal tissu...
Source: Genes - May 10, 2021 Category: Genetics & Stem Cells Authors: Anna Nowicka Pranav Pankaj Sahu Martin Kovacik Dorota Weigt Barbara Tokarz Tamar Krugman Ales Pecinka Tags: Article Source Type: research

Genes, Vol. 12, Pages 712: In Vivo Expression of Reprogramming Factor OCT4 Ameliorates Myelination Deficits and Induces Striatal Neuroprotection in Huntington ’s Disease
This study investigated the effects of in vivo expression of reprogramming factor octamer-binding transcription factor 4 (OCT4) on neural stem cell (NSC) niche activation in the subventricular zone (SVZ) and induction of cell fate specific to the microenvironment of HD. R6/2 mice randomly received adeno-associated virus 9 (AAV9)-OCT4, AAV9-Null, or phosphate-buffered saline into both lateral ventricles at 4 weeks of age. The AAV9-OCT4 group displayed significantly improved behavioral performance compared to the control groups. Following AAV9-OCT4 treatment, the number of newly generated NSCs and oligodendrocyte progenitor ...
Source: Genes - May 10, 2021 Category: Genetics & Stem Cells Authors: Ji-Hea Yu Bae-Geun Nam Min-Gi Kim Soonil Pyo Jung-Hwa Seo Sung-Rae Cho Tags: Article Source Type: research

Genes, Vol. 12, Pages 713: Expanding the Phenotypic and Genotypic Spectrum of Bietti Crystalline Dystrophy
This study reports patients affected by typical and atypical Bietti crystalline dystrophy, expanding the spectrum of this disease. This is an observational case series of patients with a clinical and molecular diagnosis of Bietti crystalline dystrophy that underwent multimodal imaging. Four unrelated patients are described with two known variants, c.802-8_810del17insGC and c.518T > G (p.Leu173Trp), and one novel missense variant, c.1169G > T (p.Arg390Leu). The patient with the novel homozygous variant had the most severe phenotype resulting in macular hole formation and retinal detachment in both eyes...
Source: Genes - May 10, 2021 Category: Genetics & Stem Cells Authors: Mariana Matioli da Palma Fabiana Louise Motta Mariana Vallim Salles Caio Henrique Marques Texeira Andr é V. Gomes Ricardo Casaroli-Marano Juliana Maria Ferraz Sallum Tags: Case Report Source Type: research

Genes, Vol. 12, Pages 705: Transcriptomic Changes in Mouse Bone Marrow-Derived Macrophages Exposed to Neuropeptide FF
In this study, the effect of NPFF on the transcriptome of mouse bone marrow-derived macrophages (BMDMs) was explored by RNA sequencing, bioinformatics, and molecular simulation. BMDMs were treated with 1 nM NPFF for 18 h, followed by RNA sequencing. Differentially expressed genes (DEGs) were obtained, followed by GO, KEGG, and PPI analysis. A total of eight qPCR-validated DEGs were selected as hub genes. Subsequently, the three-dimensional (3-D) structures of the eight hub proteins were constructed by Modeller and Rosetta. Next, the molecular dynamics (MD)-optimized 3-D structure of hub protein was acquired with Gromacs. F...
Source: Genes - May 9, 2021 Category: Genetics & Stem Cells Authors: Yulong Sun Yuanyuan Kuang Zhuo Zuo Tags: Article Source Type: research

Genes, Vol. 12, Pages 706: Variable Expressivity of the Beckwith-Wiedemann Syndrome in Four Pedigrees Segregating Loss-of-Function Variants of CDKN1C
Andrea Riccio Beckwith-Wiedemann syndrome (BWS) is an imprinting disorder characterized by prenatal and/or postnatal overgrowth, organomegaly, abdominal wall defects and tumor predisposition. CDKN1C is a maternally expressed gene of the 11p15.5 chromosomal region and is regulated by the imprinting control region IC2. It negatively controls cellular proliferation, and its expression or activity are frequently reduced in BWS. In particular, loss of IC2 methylation is associated with CDKN1C silencing in the majority of sporadic BWS cases, and maternally inherited loss-of-function variants of CDKN1C are the most frequent...
Source: Genes - May 9, 2021 Category: Genetics & Stem Cells Authors: Angela Sparago Flavia Cerrato Laura Pignata Francisco Cammarata-Scalisi Livia Garavelli Carmelo Piscopo Alessandra Vancini Andrea Riccio Tags: Case Report Source Type: research

Genes, Vol. 12, Pages 707: Expanding the Phenotypic Spectrum of PAX6 Mutations: From Congenital Cataracts to Nystagmus
Conclusions: The diagnosis of mild forms of aniridia is challenging, but these patients have a potentially blinding hereditary disease that might present with a more severe phenotype in future generations. Clinicians should be aware of the mild aniridia phenotype and request genetic testing to perform an accurate diagnosis (Source: Genes)
Source: Genes - May 9, 2021 Category: Genetics & Stem Cells Authors: Maria Nieves-Moreno Susana Noval Jesus Peralta Mar ía Palomares-Bralo Angela del Pozo Sixto Garcia-Mi ñaur Fernando Santos-Simarro Elena Vallespin Tags: Article Source Type: research

Genes, Vol. 12, Pages 701: Pediatric and Adolescent Oncofertility in Male Patients —From Alpha to Omega
This article reviews the latest information about preserving reproductive potential that can offer enhanced prospects for future conception in the pediatric male population with cancer, whose fertility is threatened because of the gonadotoxic effects of chemotherapy and radiation. An estimated 400,000 children and adolescents aged 0–19 years will be diagnosed with cancer each year. Fertility is compromised in one-third of adult male survivors of childhood cancer. We present the latest approaches and techniques for fertility preservation, starting with fertility preservation counselling, a clinical practice guideline ...
Source: Genes - May 8, 2021 Category: Genetics & Stem Cells Authors: Ovidiu B îcă Ioan S ârbu Carmen Iulia Ciongradi Tags: Review Source Type: research

Genes, Vol. 12, Pages 702: Identification and Functional Annotation of Genes Related to Bone Stability in Laying Hens Using Random Forests
In conclusion, the identified candidates represent genes that may play a role in the bone integrity of chickens. Although further studies are needed to determine causality, the genes reported here are promising in terms of alleviating bone disorders in laying hens. (Source: Genes)
Source: Genes - May 8, 2021 Category: Genetics & Stem Cells Authors: Simon Jansen Ulrich Baulain Christin Habig Faisal Ramzan Jens Schauer Armin Otto Schmitt Armin Manfred Scholz Ahmad Reza Sharifi Annett Weigend Steffen Weigend Tags: Article Source Type: research

Genes, Vol. 12, Pages 703: Characterization of ETFDH and PHGDH Mutations in a Patient with Mild Glutaric Aciduria Type II and Serine Deficiency
This study indicates that two rare autosomal recessive disorders should be considered in consanguineous families, more specifically in those with atypical presentation. (Source: Genes)
Source: Genes - May 8, 2021 Category: Genetics & Stem Cells Authors: Amanat Ali Nahid Al Dhahouri Fatmah Saeed Ali Almesmari Waseem Mahmoud Fathalla Fatma Al Jasmi Tags: Case Report Source Type: research