bluuebunny/crossref_metadata_2025_split huggingface dataset:
Expression of the cyanobacterial F0F1 ATP synthase inhibitor AtpΘ depends on small basic DNA-binding proteins and differential mRNA stability
Authors: Song Kuo , Hagemann Martin , Georg Jens , Maaß Sandra , Becher Dörte , Hess Wolfgang R. 
Published: November 2021

ABSTRACTF0F1 ATP synthases produce ATP, the universal biological energy source. ATP synthase complexes on cyanobacterial thylakoid membranes use proton gradients generated either by photosynthesis or respiration. AtpΘ is an ATP synthase regulator in cyanobacteria which is encoded by the gene atpT. AtpΘ inhibits the hydrolysis of ATP (reverse reaction) that otherwise would occur under unfavorable conditions. In the cyanobacterium Synechocystis sp. PCC 6803, AtpΘ is expressed maximum in darkness but at very low levels under optimum phototrophic growth conditions or in the presence of glucose. DNA coimmunoprecipitation experiments followed by mass spectrometry identified the binding of the two transcriptional regulators cyAbrB1 and cyAbrB2 to the promoter and the histone-like protein HU to the 5’UTR of atpT. Analyses of nucleotide substitutions in the promoter and GFP reporter assays identified a functionally relevant sequence motif resembling the HLR1 element bound by the RpaB transcription factor. Electrophoretic mobility shift assays confirmed interaction of cyAbrB1, cyAbrB2 and RpaB with the promoter DNA. However, overall the effect of transcriptional regulation was comparatively low. In contrast, atpT transcript stabilities differed dramatically, half-lives were 1.6 min in the light, 33 min in the dark and substantial changes were observed if glucose or DCMU were added. These findings show that basic transcriptional control of atpT involves nucleoid-associated DNA-binding proteins, positive regulation through RpaB, while the major effect on the condition-dependent regulation of atpT expression is mediated by controlling mRNA stability, which is related to the cellular redox and energy status.IMPORTANCEF0F1 ATP synthases are protein complexes that produce ATP, the universal biological energy source in all kinds of organisms. Under unfavorable conditions, ATP synthases can operate in a futile reverse reaction, pumping protons while ATP is used up. Cyanobacteria perform plant-like photosynthesis but they cannot use the same mechanism as plants that inhibit chloroplast ATP synthases entirely during the night because respiratory and photosynthetic complexes are both located in the same membrane system. AtpΘ is a small peptide inhibitor of the reverse ATPase function in cyanobacteria encoded by the gene atpT. The production of AtpΘ is highly regulated to ensure that it is only synthetized when it is needed. In the here presented work we found that three transcription factors contribute to the regulation of atpT expression. However, we identified the control of mRNA stability as the major regulatory process governing atpT expression. Thus, it is the interplay between transcriptional and posttranscriptional regulation that position the AtpΘ-based inhibitory mechanism within the context of the cellular redox and energy balance.
Daughter centrioles assemble preferentially towards the nuclear envelope in Drosophila syncytial embryos
Authors: Cunningham Neil H. J. , Bouhlel Imène B. , Conduit Paul T. 
Published: November 2021

AbstractCentrosomes are important organisers of microtubules within animal cells. They comprise a pair of centrioles surrounded by the pericentriolar material (PCM), which nucleates and organises the microtubules. To maintain centrosome numbers, centrioles must duplicate once and only once per cell cycle. During S-phase, a single new “daughter” centriole is built orthogonally on one side of each radially symmetric “mother” centriole. Mis-regulation of duplication can result in the simultaneous formation of multiple daughter centrioles around a single mother centriole, leading to centrosome amplification, a hallmark of cancer. It remains unclear how a single duplication site is established. It also remains unknown whether this site is pre-defined or randomly positioned around the mother centriole. Here, we show that within Drosophila syncytial embryos daughter centrioles preferentially assemble on the side of the mother facing the nuclear envelope, to which the centrosomes are closely attached. This positional preference is established early during duplication and remains stable throughout daughter centriole assembly, but is lost in centrosomes forced to lose their connection to the nuclear envelope. This shows that non-centrosomal cues influence centriole duplication and raises the possibility that these external cues could help establish a single duplication site.
The transcription factor AtHB23 modulates starch turnover for root development and plant survival under salinity
Authors: Perotti María Florencia , Arce Agustín Lucas , Ariel Federico Damián , Figueroa Carlos María , Chan Raquel Lía 
Published: November 2021

AbstractAtHB23 is a homeodomain-leucine zipper I transcription factor, previously characterized as a modulator of lateral root initiation and higher-order roots development. The role of this gene in response to salinity stress was completely unknown. To elucidate the role of AtHB23 in response to salinity stress, we combined histochemical β-glucuronidase (GUS) analysis, root phenotyping, starch staining, optic and electronic transmission microscopy, expression studies by RT-qPCR, and transcriptome analysis of silenced, overexpressor, and crossed plants. We revealed that the expression pattern of AtHB23 is regulated by NaCl in the main and lateral roots, affecting the root phenotype. A severe reduction in primary root length, a significant increment in the initiation of lateral roots, and a low survival rate in salinity conditions were observed in AtHB23-silenced plants, whereas AtHB23 overexpressors showed the opposite phenotype. These developmental defects were explained by the degradation of starch granules and an alteration in starch metabolism. The AtHB23-target gene LAX3 is repressed in the tip of the main root and affected by NaCl.We conclude that AtHB23 is vital for plant survival and adaptation to salt stress conditions, and its function is related to the gravitropic response mediated by starch granule turnover, involving the auxin carrier LAX3.HighlightThe transcription factor AtHB23 is crucial for plant survival and adaptation to salt stress conditions, and its function is related to the gravitropic response mediated by starch-granule turnover, involving LAX3.
The natural frequencies of the resting human brain: an MEG-based atlas
Authors: Capilla Almudena , Arana Lydia , García-Huéscar Marta , Melcón María , Gross Joachim , Campo Pablo 
Published: November 2021

AbstractBrain oscillations are considered to play a pivotal role in neural communication. However, detailed information regarding the typical oscillatory patterns of individual brain regions is surprisingly scarce. In this study we applied a multivariate data-driven approach to create an atlas of the natural frequencies of the resting human brain on a voxel-by-voxel basis. We analysed resting-state magnetoencephalography (MEG) data from 128 healthy adult volunteers obtained from the Open MEG Archive (OMEGA). Spectral power was computed in source space in 500 ms steps for 82 frequency bins logarithmically spaced from 1.7 to 99.5 Hz. We then applied k-means clustering to detect characteristic spectral profiles and to eventually identify the natural frequency of each voxel. Our results revealed a region-specific organisation of intrinsic oscillatory activity, following both a medial-to-lateral and a posterior-to-anterior gradient of increasing frequency. In particular, medial fronto-temporal regions were characterised by slow rhythms (delta/theta). Posterior regions presented natural frequencies in the alpha band, although with differentiated generators in the precuneus and in sensory-specific cortices (i.e., visual and auditory). Somatomotor regions were distinguished by the mu rhythm, while the lateral prefrontal cortex was characterised by oscillations in the high beta range (>20 Hz). Importantly, the brain map of natural frequencies was highly replicable in two independent subsamples of individuals. To the best of our knowledge, this is the most comprehensive atlas of ongoing oscillatory activity performed to date. Furthermore, the identification of natural frequencies is a fundamental step towards a better understanding of the functional architecture of the human brain.
The mouse mammary tumor virus intasome exhibits distinct dynamics on target DNA
Authors: Baltierra-Jasso Laura E. , Jones Nathan D. , Ballandras-Colas Allison , Engelman Alan N. , Fishel Richard , Yoder Kristine E. 
Published: November 2021

ABSTRACTRetroviral intasomes are complexes assembled from purified integrase (IN) and oligonucleotides mimicking viral DNA ends (vDNA). Recombinant intasomes faithfully recapitulate integration of vDNA into a target DNA. Structural studies of retroviral intasomes have revealed an array of IN oligomer forms, which appear to share a conserved intasome core coordinating the vDNA ends for strand transfer into the target DNA. Here we have explored the biochemical and dynamic properties of the mouse mammary tumor virus (MMTV) octameric intasome. We show that the MMTV intasome is remarkably stable compared to the prototype foamy virus (PFV) tetrameric intasome. MMTV integration activity peaks within the range of physiological ionic strength and is more active in the presence of manganese compared to magnesium. Single-molecule images demonstrate that the target DNA search by MMTV intasomes appears rate-limiting, similar to PFV intasomes. The time between strand transfer of the two MMTV vDNA ends into the target DNA is ∼3 fold slower than PFV intasomes. MMTV intasomes can form extremely stable, largely immobile filaments on a target DNA that are comprised of multiple intasomes. This unusual property suggests that MMTV intasomes may readily form higher order oligomers that might underpin their increased stability.
Myogenetic oligodeoxynucleotide restores differentiation and reverses inflammation of myoblasts aggravated by cancer-conditioned medium
Authors: Nihashi Yuma , Yamamoto Machi , Shimosato Takeshi , Takaya Tomohide 
Published: November 2021

AbstractCancer cachexia is characterized by irreversible muscle loss which is a critical factor in the prognosis of cancer patients. Myoblasts are myogenic precursor cells that are required to maintain skeletal muscle tissue. Previous studies have reported that cancer-released factors deteriorate myoblast differentiation, which is one of the causes of cachexia-associated muscle wasting. We recently identified the myogenetic oligodeoxynucleotide iSN04, which acts an anti-nucleolin aptamer and promotes myogenesis. The present study investigated the effects of iSN04 on human myoblasts exposed to conditioned medium (CM) of colon cancer cells. Cancer-CM impaired myogenic differentiation and myotube formation of myoblasts by upregulating the expression of inflammatory cytokines. iSN04 completely reversed cancer-CM-induced deteriorated myogenesis and inflammatory responses in myoblasts. Tumor necrosis factor-α (TNF-α), a representative cytokine present in cancer-CM, inhibited differentiation and induced inflammation of myoblasts, similar to cancer-CM. Pre-treatment with iSN04 reversed TNF-α-induced cachectic phenotypic features in myoblasts. These results indicate that iSN04 protects myoblasts against the effects of cancer-released factors and maintain their myogenic activity. This study provides a novel therapeutic strategy to prevent muscle loss associated with cancer cachexia.
Mechanical torque promotes bipolarity of the mitotic spindle through multi-centrosomal clustering
Authors: Miles Christopher E. , Zhu Jie , Mogilner Alex 
Published: November 2021

AbstractIntracellular forces shape cellular organization and function. One example is the mi-totic spindle, a cellular machine consisting of multiple chromosomes and centrosomes which interact via dynamic microtubule filaments and motor proteins, resulting in complicated spatially dependent forces. For a cell to divide properly, is important for the spindle to be bipolar, with chromosomes at the center and multiple centrosomes clustered into two ‘poles’ at opposite sides of the chromosomes. Experimental observations show that in unhealthy cells, the spindle can take on a variety of patterns. What forces drive each of these patterns? It is known that attraction between centrosomes is key to bipolarity, but what the prevents the centrosomes from collapsing into a monopolar configuration? Here, we explore the hypothesis that torque rotating chromosome arms into orientations perpendicular to the centrosome-centromere vector promotes spindle bipolarity. To test this hypothesis, we construct a pairwise-interaction model of the spindle. On a continuum version of the model, an integro-PDE system, we perform linear stability analysis and construct numerical solutions which display a variety of spatial patterns. We also simulate a discrete particle model resulting in a phase diagram that confirms that the spindle bipolarity emerges most robustly with torque. Altogether, our results suggest that rotational forces may play an important role in dictating spindle patterning.
Impact of pre-anthesis drought stress on physiology, yield-related traits and drought responsive genes in green super rice
Authors: Ahmad Hassaan , Zafar Syed Adeel , Naeem Muhammad Kashif , Shokat Sajid , Inam Safeena , Naveed Amir Shahzad , Xu Jianlong , Li Zhikhang , Ali Ghulam Muhammad , Khan Muhammad Ramzan 
Published: November 2021

ABSTRACTOptimum soil water availability is vital for maximum yield production in rice which is challenged by increasing spells of drought. The reproductive stage drought is among the main limiting factors leading to the drastic reduction in grain yield. Objective of this study was to investigate the molecular and morpho-physiological responses of pre-anthesis stage drought stress in green super rice. The study assessed the performance of 26 rice lines under irrigated and drought conditions. Irrigated treatment was allowed to grow normally while drought stress was imposed for 30 days at pre-anthesis stage. Three important physiological traits including pollen fertility percentage (PFP), cell membrane stability (CMS) and normalized difference vegetative index (NDVI) were recorded at anthesis stage during the last week of drought stress. Agronomic traits of economic importance including grain yield were recorded at maturity stage. The analysis of variance demonstrated significant variation among the genotypes for most of the studied traits. Correlation and principal component analyses demonstrated highly significant associations of particular agronomic traits with grain yield, and genetic diversity among genotypes, respectively. Our study demonstrated a higher drought tolerance potential of GSR lines compared to local cultivars, mainly by higher pollen viability, plant biomass, CMS, and harvest index under drought. In addition, the molecular basis of drought tolerance in GSR lines was related to upregulation of certain drought responsive genes includingOsSADRI, OsDSM1, andOsDT11. Our study identified novel drought tolerance related genes (OsDRG-1, OsDRG-2, OsDRG-3andOsDRG-4)that could be further characterized using reverse genetics to be utilized in molecular breeding for drought tolerance.
Gene Discovery Using Computational and Microarray Analysis of Transcription in the Drosophila melanogaster Testis
Authors: Andrews Justen , Bouffard Gerard G. , Cheadle Chris , Lü Jining , Becker Kevin G. , Oliver Brian 
Published: November 2021

Identification and annotation of all the genes in the sequencedDrosophila genome is a work in progress. Wild-type testis function requires many genes and is thus of potentially high value for the identification of transcription units. We therefore undertook a survey of the repertoire of genes expressed in the Drosophilatestis by computational and microarray analysis. We generated 3141 high-quality testis expressed sequence tags (ESTs). Testis ESTs computationally collapsed into 1560 cDNA set used for further analysis. Of those, 11% correspond to named genes, and 33% provide biological evidence for a predicted gene. A surprising 47% fail to align with existing ESTs and 16% with predicted genes in the current genome release. EST frequency and microarray expression profiles indicate that the testis mRNA population is highly complex and shows an extended range of transcript abundance. Furthermore, >80% of the genes expressed in the testis showed onefold overexpression relative to ovaries, or gonadectomized flies. Additionally, >3% showed more than threefold overexpression at p <0.05. Surprisingly, 22% of the genes most highly overexpressed in testis matchDrosophila genomic sequence, but not predicted genes. These data strongly support the idea that sequencing additional cDNA libraries from defined tissues, such as testis, will be important tools for refined annotation of the Drosophila genome. Additionally, these data suggest that the number of genes in Drosophila will significantly exceed the conservative estimate of 13,601.[The sequence data described in this paper have been submitted to the dbEST data library under accession nos.AI944400–AI947263 and BE661985–BE662262.][The microarray data described in this paper have been submitted to the GEO data library under accession nos. GPLS, GSM3–GSM10.]
Distribution of Protein Folds in the Three Superkingdoms of Life
Authors: Wolf Yuri I. , Brenner Steven E. , Bash Paul A. , Koonin Eugene V. 
Published: November 2021

A sensitive protein-fold recognition procedure was developed on the basis of iterative database search using the PSI-BLAST program. A collection of 1193 position-dependent weight matrices that can be used as fold identifiers was produced. In the completely sequenced genomes, folds could be automatically identified for 20%–30% of the proteins, with 3%–6% more detectable by additional analysis of conserved motifs. The distribution of the most common folds is very similar in bacteria and archaea but distinct in eukaryotes. Within the bacteria, this distribution differs between parasitic and free-living species. In all analyzed genomes, the P-loop NTPases are the most abundant fold. In bacteria and archaea, the next most common folds are ferredoxin-like domains, TIM-barrels, and methyltransferases, whereas in eukaryotes, the second to fourth places belong to protein kinases, β-propellers and TIM-barrels. The observed diversity of protein folds in different proteomes is approximately twice as high as it would be expected from a simple stochastic model describing a proteome as a finite sample from an infinite pool of proteins with an exponential distribution of the fold fractions. Distribution of the number of domains with different folds in one protein fits the geometric model, which is compatible with the evolution of multidomain proteins by random combination of domains.[Fold predictions for proteins from 14 proteomes are available on the World Wide Web atftp://ncbi.nlm.nih.gov/pub/koonin/FOLDS/index.html. The FIDs are available by anonymous ftp at the same location.]
Comparative Sequence of Human and Mouse BAC Clones from the mnd2 Region of Chromosome 2p13
Authors: Jang Wonhee , Hua Axin , Spilson Sandra V. , Miller Webb , Roe Bruce A. , Meisler Miriam H. 
Published: November 2021

The mnd2 mutation on mouse chromosome 6 produces a progressive neuromuscular disorder. To determine the gene content of the 400-kb mnd2 nonrecombinant region, we sequenced 108 kb of mouse genomic DNA and 92 kb of human genomic sequence from the corresponding region of chromosome 2p13.3. Three genes with the indicated sizes and intergenic distances were identified:D6Mm5e (⩾81 kb)–787 bp–DOK (2 kb)–845 bp–LOR2 (⩾6 kb). D6Mm5e is expressed in many tissues at very low abundance and the predicted 526-residue protein contains no known functional domains. DOK encodes the p62dok rasGAP binding protein involved in signal transduction. LOR2 encodes a novel lysyl oxidase-related protein of 757 amino acid residues. We describe a simple search protocol for identification of conserved internal exons in genomic sequence. Evolutionary conservation proved to be a useful criterion for distinguishing between authentic exons and artifactual products obtained by exon amplification, RT–PCR, and 5′ RACE. Conserved noncoding sequence elements longer than 80 bp with ⩾75% nucleotide sequence identity comprise ∼1% of the genomic sequence in this region. Comparative analysis of this human and mouse genomic DNA sequence was an efficient method for gene identification and is independent of developmental stage or quantitative level of gene expression.[The sequence data described in this paper have been submitted to the GenBank data library under the following accession numbers: AC003061, mouse BAC clone 245c12; AC003065, human BAC clone h173(E10); AF053368, mouse Lor2 cDNA; AF084363, 108-kb contig from mouse BAC 245c12; AF084364, mouse D6Mm5ecDNA.]
Postsynaptic α-Neurotoxin Gene of the Spitting Cobra, Naja naja sputatrix: Structure, Organization, and Phylogenetic Analysis
Authors: Afifiyan Fatemeh , Armugam Arunmoziarasi , Tan Chee Hong , Gopalakrishnakone Ponnampalam , Jeyaseelan Kandiah 
Published: November 2021

The venom of the spitting cobra, Naja naja sputatrixcontains highly potent α-neurotoxins (NTXs) in addition to phospholipase A2 (PLA2) and cardiotoxin (CTX). In this study, we report the complete characterization of three genes that are responsible for the synthesis of three isoforms of α-NTX in the venom of a single spitting cobra. DNA amplification by long-distance polymerase chain reaction (LD-PCR) and genome walking have provided information on the gene structure including their promoter and 5′ and 3′ UTRs. Each NTX isoform is ∼4 kb in size and contains three exons and two introns. The sequence homology among these isoforms was found to be 99%. Two possible transcription sites were identified by primer extension analysis and they corresponded to the adenine (A) nucleotide at positions +1 and −45. The promoter also contains two TATA boxes and a CCAAT box. Putative binding sites for transcriptional factors AP-2 and GATA are also present. The high percentage of similarity observed among the NTX gene isoforms of N. n. sputatrix as well as with the α-NTX and κ-NTX genes from other land snakes suggests that the NTX gene has probably evolved from a common ancestral gene.[The genomic DNA sequences reported in this paper have been submitted to GenBank databases under accession nos. AF096999 to AF097001.]