Compartmentalized regulation of organelle integrity in neurodegenerative diseases:lessons from the Drosophila motor neuron

Neurons are highly polarized,morphologically asymmetric,and functionally compartmentalized cells that contain long axons extending from the cell body.For this reason,their maintenance relies on spatiotemporal regulation of organelle distribution between the somatodendritic and axonal domains.Although some organelles,such as mitochondria and smooth endoplasmic reticulum,are widely distributed throughout the neuron,others are segregated to either the somatodendritic or axonal compartment.For example,Golgi outposts and acidified lysosomes are predominantly present in the somatodendritic domain and rarely distributed along the axon,whereas newly formed autophagosomes and synaptic vesicles are mainly distributed in the distal axon(Britt et al.,2016).

ATF6 aggravates apoptosis in early porcine embryonic development by regulating organelle homeostasis under high-temperature conditions

Activating transcription factor 6(ATF6),one of the three sensor proteins in the endoplasmic reticulum(ER),is an important regulator of ER stress-induced apoptosis.ATF6 resides in the ER and,upon activation,is translocated to the Golgi apparatus,where it is cleaved by site-1 protease(S1P)to generate an amino-terminal cytoplasmic fragment.Although recent studies have made progress in elucidating the regulatory mechanisms of ATF6,its function during early porcine embryonic development under high-temperature(HT)stress remains unclear.In this study,zygotes were divided into four groups:control,HT,HT+ATF6 knockdown,and HT+PF(S1P inhibitor).Results showed that HT exposure induced ER stress,which increased ATF6 protein expression and led to a decrease in the blastocyst rate.Next,ATF6 expression was knocked down in HT embryos under microinjection of ATF6 double-stranded RNA(dsRNA).Results revealed that ATF6 knockdown(ATF6-KD)attenuated the increased expression of CHOP,an ER stress marker,and Ca2+release induced by HT.In addition,ATF6-KD alleviated homeostasis dysregulation among organelles caused by HT-induced ER stress,and further reduced Golgi apparatus and mitochondrial dysfunction in HT embryos.AIFM2 is an important downstream effector of ATF6.Results showed that ATF6-KD reduced the occurrence of AIFM2-mediated embryonic apoptosis at HT.Taken together,our findings suggest that ATF6 is a crucial mediator of apoptosis during early porcine embryonic development,resulting from HT-induced ER stress and disruption of organelle homeostasis.

Analysis on the Relationship between Selective Pressure and Nucleotide Substitution Rate in Nucleus and Organelle Genes of Sorghum and Maize

[Objective]The aim was to research the relationship between nucleotide substitutions rate and selective pressure.[Method]Synonymous and nonsynonymous substitutions and their ratios for some sorghum and maize genes in nucleus and organelle genomes were analyzed by statistical method,and comparative analysis of related functional genes were carried out.[Result]The pure selective pressures of the related functional genes were similar between nucleus and chloroplast genomes,but was lower in mitochondrial genome.The significant differences of nucleotide substitution rate between sorghum and maize orthologous genes in nucleus genome,and among different functional genes in nucleus genome were mainly due to the nonsynonymous substitution difference.[Conclusion]The molecular evolutional rate of different functional genes and different lineages were influenced by selective pressure.The differences of molecular evolutional rate among nucleus,chloroplast and mitochondria genomes had no direct relationship with selective pressure.

Protective Actions of Blumea Flavanones on Primary Cultured Hepatocytes and Liver Subcellular Organelle against Lipid Peroxidation

To search for the protective actions of blumea flavanones (BFs) on hepatocytes and hepatic subcellular organelle against lipid peroxidation, monkey′s hepatocytes were isolated and cultured with or without blumea flavanones, then damaged by FeSO 4 cysteine or CCl 4. The lipid peroxidation (malondialdehyde production) and alteration in hepatocyte membrane (leakage of GPT) were estimated. Hepatic subcellular organelles were also isolated and incubated with or without blumea flavanones, then injured by FeSO 4 ascorbate. The generation of malondialdehyde(MDA) was measured. It was found that BFs 10 and 100 μmol·L 1 inhibited the MDA generation and GPT (glutamic pyruvic transaminase) leakage out of hepatocytes that were induced by CCl 4 or FeSO 4 cysteine. BFs could prevent lipid peroxidation initiated by FeSO 4 ascorbate in subcellular organelle suspension. Among BFs, BF 2 possessed the strongest activity. Conclusion: Blumea flavanones possess antioxidation activities that protect monkey′s hepatocytes and hepatic subcellular organelle against injuries induced by FeSO4 or CCl 4.

Codon evolution in double-stranded organelle DNA: strong regulation of homonucleotides and their analog alternations

In our previous study, complete single DNA strands which were obtained from nuclei, chloroplasts and plant mitochondria obeyed Chargaff’s second parity rule, although those which were obtained from animal mitochondria deviated from the rule. On the other hand, plant mitochondria obeyed another different rule after their classification. Complete single DNA strand sequences obtained from chloroplasts, plant mitochondria, and animal mitochondria, were divided into the coding and non-coding regions. The non-coding region, which was the complementary coding region on the reverse strand, was incorporated as a coding region in the forward strand. When the nucleotide contents of the coding region or non-coding regions were plotted against the composition of the four nucleotides in the complete single DNA strand, it was determined that chloroplast and plant mitochondrial DNA obeyed Chargaff’s second parity rule in both the coding and non-coding regions. However, animal mitochondrial DNA deviated from this rule. In chloroplast and plant mitochondrial DNA, which obey Chargaff’s second parity rule, the lines of regression for G (purine) and C (pyrimidine) intersected with regression lines for A (purine) and T (pyrimidines), respectively, at around 0.250 in all cases. On the other hand, in animal mitochondrial DNA, which deviates from Chargaff’s second parity rule, only regression lines due to the content of homonucleotides or their analogs in the coding or non-coding region against those in the complete single DNA strand intersected at around 0.250 at the horizontal axis. Conversely, the intersection of the two lines of regression (G and A or C and T) against the contents of heteronucleotides or their analogs shifted from 0.25 in both coding and non-coding regions. Nucleotide alternations in chloroplasts and plant mitochondria are strictly regulated, not only by the proportion of homonucleotides and their analogs, but also by the heteronucleotides and their analogs. They are strictly regulated in animal mitochondria only by the content of homonucleotides and their analogs.

De Novo Organelle Biogenesis in the Cyanobacterium TDX16 Released from the Green Alga <i>Haematococcus pluvialis</i>

It is believed that eukaryotes arise from prokaryotes, which means that organelles can form de novo in prokaryotes. Such events, however, had not been observed previously. Here, we report the biogenesis of organelles in the endosymbiotic cyanobacterium TDX16 (prokaryote) that was released from its senescent/necrotic host cell of green alga Haematococcus pluvialis (eukaryote). Microscopic observations showed that organelle biogenesis in TDX16 initiated with cytoplasm compartmentalization, followed by de-compartmentalization, DNA allocation, and re-compartmentalization, as such two composite organelles-the primitive chloroplast and primitive nucleus sequestering minor and major fractions of cellular DNA respectively were formed. Thereafter, the eukaryotic cytoplasmic matrix was built up from the matrix extruded from the primitive nucleus;mitochondria were assembled in and segregated from the primitive chloroplast, whereby the primitive nucleus and primitive chloroplast matured into the nucleus and chloroplast respectively. While mitochondria subsequently turned into double-membraned vacuoles after matrix degradation. Results of pigment analyses, 16S rRNA and genome sequencing revealed that TDX16 is a phycocyanin-containing cyanobacterium resembling Chroococcidiopsis thermalis, which had acquired 9,017,401 bp DNAs with 10,301 genes from its host. Accordingly, we conclude that organelle biogenesis in TDX16 is achieved by hybridizing the acquired eukaryotic DNAs with its own one and expressing the hybrid genome. The formation of organelles in cyanobacterium TDX16 is the first case of organelle biogenesis in prokaryotes observed so far, which sheds an unprecedented light on eukaryotes and their connections with prokaryotes, and thus has broad implications on biology.

Complete organelle genomes of Sinapis arvensis and their evolutionary implications

Sinapis arvensis,belonging to the genus Sinapis of the family Brassicaceae,has good agronomic characters that make it a valuable genetic resource for crop improvement and is a cytoplasmic source of heterologous cytoplasmic male sterility(CMS).In addition,S.arvensis has played an important role in the evolution of the six major cultivated Brassica species involved in the triangle of U.Using next-generation sequencing,we assembled and revealed the gene composition of S.arvensis cytoplasmic genome.The chloroplast genome comprises 153,590 bp,with 112 individual genes,including 4 r RNA,29 t RNA,and 79 proteincoding genes.The mitochondrial genome comprises 240,024 bp,with 54 genes,including 18 t RNA,three r RNA and 33 protein-coding genes.Genome structure and evolutionary analysis indicated that the sequences of the S.arvensis organellar genomes were more similar to those of Brassica nigra and B.carinata than to those of other Brassicaceae species.Four mitochondrial open reading frames displaying chimeric structural features and encoding hypothetical proteins with transmembrane domains may account for the infertility of Nsa CMS previously derived from somatic cell hybridization between B.napus and S.arvensis.These results will not only contribute to utilize the germplasm resource of S.arvensis,and comprehend the evolution of organelle genomes within the Brassicaceae family,but also help to identify genes conditioning the alloplasmic male sterility of Nsa CMS in B.napus.

Glyphosate exposure deteriorates oocyte meiotic maturation via induction of organelle dysfunctions in pigs

Background:Recently,defects in mammalian oocytes maturation induced by environmental pollution results in the decreasing animal reproduction.Animal exposed to glyphosate is largely unavoidable because glyphosate is one of the most widely used herbicide worldwide due to its high-efficiency and broad-spectrum effects,which causes glyphosate an environmental contaminant found in soil,water and food.During the last few years,the growing and wider use of glyphosate has raised great concerns about its effects of reproductive toxicity.In this study,using porcine models,we investigated effects of glyphosate on organelle functions during oocyte meiosis.Results:The results showed glyphosate exposure disrupted porcine oocyte maturation.Expression levels of cumulus expansion-related genes were interfered,further indicating the meiotic defects.The damaging effects were mediated by destruction of mitochondrial distribution and functions,which induced ROS accumulation and oxidative stress,also indicated by the decreased mRNA expression of related antioxidant enzyme genes.We also found an interference of endoplasmic reticulum(ER)distribution,disturbance of Ca^(2+)homeostasis,as well as fluctuation of ER stress,showing with the reduced ER stress-related mRNA or protein expression,which could indicate the dysfunction of ER for protein processing and signal transduction in glyphosate-exposed oocytes.Moreover,glyphosate exposure induced the disruption of lysosome function for autophagy,showing with the decrease of LAMP2 expression and autophagy-related genes mRNA expression.Additionally,our data showed the distribution of Golgi apparatus and the functions of ribosome were disturbed after glyphosate exposure,which might affect protein synthesis and transport.Conclusions:Collectively,our study showed that exposed to glyphosate could affect animal reproduction by compromising the quality of oocytes through its wide toxic effects on organelle functions.

Prediction of Monophyletic Groups Based on Gene Order and Sequence Similarity in Organelle DNA

Organelle genomics has become its own field of study. Much information can be gleaned from the study of cell organelles. The differences in the genomes of organelles, such as the mitochondrion and the chloroplast are amenable to phylogenetic and cladistic studies. These differences include the genome sequence, GC%, genome length and gene order. The conserved nature of the organelle genomes and the gene inventory of both mitochondrial and chloroplast genomes also make this easier to accomplish. This paper includes a review of existing organelle genome software. These include gene annotation and genome visualization tools as well as organelle gene databases for both mitochondrion and plastid. A new R tool, available on github, called “Organelle DNA Lineages”, or ODL, was written to compare and classify organelle genomes based on their genome sequence and gene order. The software was run on the mitochondrial genomes of a set of 51 cephalopod species, delineating ten separate monophyletic groups, including argonauts, nautiluses, octopuses, cuttlefish, and six squid groups. This new tool can help enrich and expand the field of organelle genomics.

Structural features of the nucleotide sequences of virus and organelle genomes

The four nucleotides (bases), A, T (U), G and C in small genomes, virus DNA/RNA, organelle and plastid genomes were also arranged sophisticatedly in the structural features in a single-strand with 1) reverse-complement symmetry of base or base sequences, 2) bias of four bases, 3) multiple fractality of the distribution of each four bases depending on the distance in double logarithmic plot (power spectrum) of L (the distance of a base to the next base) vs. P (L) (the probability of the base-distribution at L), although their genomes were composed of low numbers of the four bases, and the base-symmetry was rather lower than the prokaryotic-and the eukaryotic cells. In the case of the genomic DNA composed of less than 10,000 nt, it was better than to be partitioned at 10 of the L-value, and the structural features for the biologically active genomic DNA were observed as the large genomes. As the results, the base sequences of the genomic DNA including the genomic-RNA might be universal in all genomes. In addition, the relationship between the structural features of the genome and the biological complexity was discussed.

Neurodegeneration and Mitochondria Organelle Transplantation: “A Technology That Proof of Principle Suggest Is Ready for Prime Time”

It is known that mitochondrial dysfunction is associated with neurodegenerative diseases including amyotrophic lateral sclerosis (ALS). Researchers have tested the therapeutic efficacy of many mitochondrial targeted agents;however, results have been disappointing without significant impact on disease survival. Several groups have demonstrated that mitochondrial transfer of isolated normal healthy mitochondria to defective calls can restore functional recovery. Our experience with mitochondria organelle transplantation (MOT) in cancer cells led to investigating the technology for neurodegenerative diseases (NDs), especially ALS. The rationale was that if the uptake of normal mitochondria into cancer cells inhibited proliferation and glycolysis;then MOT might be a cell-based therapy for NDs. In this communication, we will present background research on MOT in vitro and in vivo cell culture and animal models respectively. This research evidence showed proof of principle of the technology. This fact led us to try the procedure on a desperate human ALS patient.

Development of organelle single nucleotide polymorphism (SNP) markers and their application for the identification of cytoplasmic inheritance patterns in Pyropia yezoensis (Bangiales,Rhodophyta)

The genus Pyropia contains several important cultivated species.Genetic research in nori species has mainly focused on the cell nucleus,with few studies on organelles(chloroplast and mitochondria).Due to the high copy numbers of organelles in cells,which influence the development and traits of algae,it is necessary to study their genetic mechanism.In this study,the marine red alga Pyropia yezoensis,an important economic macroalga,was selected as the study object.To investigate organelle(chloroplast and mitochondria)inheritance in P.yezoensis,the wild type RZ(maternal strain)was crossed with the red mutant HT(paternal strain)and 30 color-sectors from 11 F1 gametophytic blades were examined.The complete chloroplast and mitochondrial genomes of the red mutant(HT)were assembled for the first time.One reliable and stable single nucleotide polymorphism(SNP)loci filtrated by bioinformatics analysis was used as a molecular marker for chloroplast and mitochondrial DNA,respectively,in subsequent experiments.PCR amplification and sequence analysis showed that the haplotypes of color-sectors detected were consistent with those of the maternal parent,confirming that both chloroplast and mitochondrial genomes were inherited maternally in P.yezoensis.The inheritance pattern of organelles in P.yezoensis can be used to guide the hybridization and breeding of nori.Additionally,the organelle SNP markers developed in this study can be applied in subsequent genetic research.

Organelle Structures: Bridging Strategy and Technological Processes

The shifting requirements as imposed on operations ma nagement require adjusting and tailoring the organisational structure to meet ma rket demands. However, translating these requirements directly into hierarchical structure will not ensure the integration of processes across organisational un its and guarantee desirable performance. Therefore, management and management li terature wonders: · How should we connect processes to the external environment within a strategi c framework · Which organisational structures do meet performance requirements · Which choices and freedom do we have within organisational structures · How and when do we implement organisational structures That the hierarchical structure does not meet as such the performance requiremen ts nor did it relate to these became already clear during case studies performed in the ’70s. The conclusion was drawn that organisational changes should affect working processes before they proof to be viable. This required the development of new approach through empirical studies and base d on literature. This led to the development of the organelle structure. The org anelle structure should connect to the strategy and the product flow. Thereto, a decision model has been developed for revealing these relations and the practic al implication. During a number of case studies this methodology has been refined and includes t he strategic choice between variants for the organelle structure with their own performance capabilities; we distinguish about 20 variants ranging between the f unctional organisation and the product flow organisation. These ranges of choice s however can be connected to different order entry points, stemming from logist ic concepts. This extends the performance to improved lead-times and improved c ontrol. Strategic choices relate the organelle structure to external performance criteria dictated by product/market-combinations: · lead-time · quality · costs and internal choices for performance criteria: · flexibility · productivity · resource utilisation · innovative performance. Case studies reveal the drastic improvements of the performance of operations an d manufacturing. The paper will discuss a few of these implementations to demons trate the impact. They also show how one derives the hierarchical structure from the choice for the organelle structure. Organelle structures do bridge the link of an industrial company to its environm ent and the internal possibilities, dictated by characteristics of product flow and process execution. The link to the environment results in a strategic framew ork for assessment of alternatives and possibilities. Choices for organelle stru ctures depend strongly on choices on the order entry points of the hardware flow and the specification flow. The evaluation of the characteristics takes place a gainst the strategic framework ensuring competitive advantage as well as a high probability of factual implementation and performance improvement.

Mitochondrial Organelle Transplantation Is a Potential Therapeutic for Mitochondria Dysfunction in Severe Acute Respiratory Syndrome (SARS) Coronavirus Diseases

COVID-19 severe symptoms and high mortality are mainly seen in elders with age-associated diseases who have mitochondrial dysfunction. Mitochondrial dysfunction is a vulnerability and comorbidity of COVID-19. Cytokine storm, and increased serum iron and ferritin and reactive oxygen species (ROS) in COVID-19 further damage mitochondria. Amelioration of mitochondrial dysfunction may be a strategy of prevention and treatment of COVID-19. We also describe mitochondrial organelle transplantation (MOT) which has restored mitochondrial function, improved the repair of injured tissues and suppressed hyperinflammation in life-threatening sepsis. MOT is a potential therapy for severe COVID-19. Finally, we report the first case of MOT for a severe COVID-19 patient. MOT is safe and might have beneficial effect on the severe COVID-19.

Lipid-Protein Microinclusions in the Morphological Structures of Organelle Membranes Studied by Fluorescent Confocal Microscopy

Peculiar properties of morphological structures of organelle membranes were studied by fluorescent confocal microscopy. The list of objects in our experiments was represented by mitochondria, chloroplasts and vacuoles. During this study, identification of lipid microinclusions having the form of such lipid-protein structural microformations as lipid-protein microdomains, vesicles and membrane tubular structures (cytoplasmic transvacuolar strands and nanotubes) located in organelle membranes or bound up with them was conducted. Such membrane probes as laurdan, DPH, ANS and bis-ANS were used. Comparison of fluorescence intensity of these membrane probes was conducted. This investigation of the morphological properties of lipid-protein structural microformations was accompanied with analysis of 1) the phase state and 2) dynamics of microviscosity variations in the membrane elements of isolated plant cell organelles. Distributions of laurdan fluorescence generalized polarization (GP) values for the membrane on the whole and for the intensively fluorescing membrane segments were obtained. It was discovered that the microviscosity of intensively fluorescing membrane segments essentially differed from the microviscosity of the rest part of the membrane. In conclusion, some results of the study of peculiar properties of lipid-protein structural microformations related to the structure of organelle membranes and the discoveries made in this investigation are discussed.

An efficient approach for obtaining plant organelle genomes

Plant organelle(plastid and mitochondrial)genomes contain substantial information for plant evolution and adaptation.Therefore,it’s important to reveal plant whole-genome sequences including plastid and mitochondrial genomes.To decode these sequences,it is required to efficiently separate organelle genomic DNA from nucleus genome,which is difficult and laborious.In this study,an efficient procedure was established to obtain plant organelle genomes without extraction of plastid and mitochondria.Organelle DNA was extracted from three materials including Sinapis arvensis var.‘Yeyou 18’,a cytoplasmic male sterile line(Nsa CMS)and its corresponding maintainer line‘Zhongshuang 4’.DNA was sequenced by Roche 454 FLXt and Illumina Miseq platforms.Organelle genomes were assembled using the generated reads and public organelle genome sequences.This research presented a procedure that efficiently assembled organelle genomes and subsequent fill gaps by extending the consensus contig terminals.This method enabled us to assemble plant plastid and mitochondrial genomes simultaneously.The obtained organelle genomes could accelerate understanding of mitochondrial rearrangements and laid a foundation for further study of Sinapis arvensis evolution and sterility gene of Nsa CMS.

急性胰腺炎的发病机制研究进展及未来展望

急性胰腺炎(acute pancreatitis,AP)是消化系统常见急腹症之一,发病率在我国和欧美各国均呈逐年上升趋势。尽管病因多种多样,但均遵循特定的病理生理学过程且其中的关键调控分子具有相似性。近年来,一方面以胰腺腺泡和导管上皮细胞为主要研究对象,聚焦钙信号通路、自噬流受损、线粒体等细胞器功能障碍、内质网应激失衡取得了不少重要进展;另一方面聚焦免疫细胞的早期募集和过度活化参与调控全身炎症反应的发生及胰腺坏死和胰腺炎相关器官功能不全开展了不少前沿研究。上述研究发现大大增进了我们对AP发病机制和干预策略的理解和认识。本文将重点讨论近年来AP发病机制的基础研究进展,以期对AP的早期治疗提供临床指导。

ORPA:a fast and efficient phylogenetic analysis method for constructing genome-wide alignments of organelle genomes

Creating a multi-gene alignment matrix for phylogenetic analysis using organelle genomes involves aligning single-gene datasets manually,a process that can be time-consuming and prone to errors.The HomBlocks pipeline has been created to eliminate the inaccuracies arising from manual operations.The processing of a large number of sequences,however,remains a time-consuming task.To conquer this challenge,we develop a speedy and efficient method called Organelle Genomes for Phylogenetic Analysis(ORPA).ORPA can quickly generate multiple sequence alignments for whole-genome comparisons by parsing the result files of NCBI BLAST,completing the task just in 1 min.With increasing data volume,the efficiency of ORPA is even more pronounced,over 300 times faster than HomBlocks in aligning 60 high-plant chloroplast genomes.The phylogenetic tree outputs from ORPA are equivalent to HomBlocks,indicating its outstanding efficiency.Due to its speed and accuracy,ORPA can identify species-level evolutionary conflicts,providing valuable insights into evolutionary cognition.

热带假丝酵母β-紫罗兰酮工程菌的构建及其发酵优化

β-紫罗兰酮是一种来源于植物的不规则单萜化合物,具有良好的驱虫、抗菌、抗癌和抗氧化等生物活性,广泛应用于农业、食品、医药和香精香料等行业。热带假丝酵母是潜在的萜类高效合成底盘细胞。为了提高β-紫罗兰酮产量,该研究在课题组前期构建的β-紫罗兰酮工程菌的基础上,通过酶的亚细胞区室组合,构建了一株β-紫罗兰酮合成关键基因PhCCD1,同时在其胞质、过氧化物酶体和脂滴表达的β-紫罗兰酮工程菌PCL-01;然后,对其摇瓶发酵培养基装液量、培养基碳氮比、发酵温度和辅因子Fe^(2+)浓度等条件进行优化;最后进行5 L发酵罐小试。工程菌PCL-01的β-紫罗兰酮摇瓶产量为152.4 mg/L,较出发菌株增加50%;经过摇瓶发酵优化,β-紫罗兰酮产量为185.8 mg/L,提升22%;最后,在5 L发酵罐上可达403.9 mg/L。该研究对于其他萜类物质合成的菌株代谢改造具有借鉴意义,亦可为其他菌种发酵性能的研究提供参考价值。

细胞器超分辨成像荧光染料

超分辨显微镜提供超越传统光学显微镜衍射极限的成像能力,彻底改变了细胞生物学领域研究。在这一背景下,具有光稳定性、易于修饰和荧光开关可调等独特性能的有机小分子染料获得了新的发展机遇。聚焦于不同细胞器超分辨成像荧光染料,总结了目前可用的超分辨荧光探针的设计和靶向策略。首先简要介绍了三种主要的超分辨成像技术,包括结构光照明显微镜技术、受激发射损耗显微技术和单分子定位成像技术,以及它们对荧光染料性能的不同要求,并介绍了近五年来用于线粒体、溶酶体、细胞膜、脂滴和细胞核的超分辨成像的荧光染料。最后讨论了该领域当前所面临的挑战。