Biology subjects

Zhu, D.

Publications and source records attributed to Zhu, D..

At least 91 records · Page 5Linked to original sources

bioRxiv2021

Ultra-deep through-skull mouse brain imaging via the union of skull optical clearing and three-photon microscopy

Optical microscopy has enabled in vivo monitoring of brain structures and functions with high spatial resolution. However, the strong optical scattering in turbid brain tissue and skull impedes the observation of microvasculature and neuronal structures at a large depth. Herein, we proposed a strategy to overcome the influence induced by the high scattering effect of both skull and brain tissue via the combination of skull optical clearing (SOC) technique and thee-photon fluorescence microscopy (3PM). The Visible-NIR-II compatible Skull Optical Clearing Agents (VNSOCA) we applied reduced the skull scattering and water absorption in long wavelength by refractive index matching and H2O replacement to D2O respectively. 3PM with the excitation in the 1300-nm window reached 1.5 mm cerebrovascular imaging depth in cranial window. Combining the two advanced technologies together, we achieved so far the largest cerebrovascular imaging depth of 1.0 mm and neuronal imaging depth of >700 m through intact mouse skull. Dual-channel through-skull imaging of both brain vessels and neurons was also successfully realized, giving an opportunity of non-invasively monitoring the deep brain structures and functions at single-cell level simultaneously.

neuroscience↗

bioRxiv2021

GraphPrompt: Biomedical Entity Normalization Using Graph-based Prompt Templates

Biomedical entity normalization unifies the language across biomedical experiments and studies, and further enables us to obtain a holistic view of life sciences. Current approaches mainly study the normalization of more standardized entities such as diseases and drugs, while disregarding the more ambiguous but crucial entities such as pathways, functions and cell types, hindering their real-world applications. To achieve biomedical entity normalization on these under-explored entities, we first introduce an expert-curated dataset OBO-syn encompassing 70 different types of entities and 2 million curated entity-synonym pairs. To utilize the unique graph structure in this dataset, we propose GraphPrompt, a promptbased learning approach that creates prompt templates according to the graphs. Graph-Prompt obtained 41.0% and 29.9% improvement on zero-shot and few-shot settings respectively, indicating the effectiveness of these graph-based prompt templates. We envision that our method GraphPrompt and OBO-syn dataset can be broadly applied to graph-based NLP tasks, and serve as the basis for analyzing diverse and accumulating biomedical data.

bioinformatics↗

bioRxiv2021

Global distribution of mammal herbivore biomass reveals megafauna extinction patterns

Mammalian herbivores strongly shape Earth system processes. A lack of global dynamic models of mammal populations limits our understanding of their ecological role at large scales and the consequences of their extinctions. We developed a mechanistic global model of terrestrial herbivore populations simulated with 37 functional groups defined by analyzing eco-physiological traits of all extant herbivores (n = 2599). We coupled this model with a global vegetation model to predict herbivores biomass maximum potential (pre-industrial) and at present. Natural ecosystems could have sustained a wild herbivore wet biomass of 330 Mt, comprised of 192 Mt by large (body mass > 5 kg) and 138 Mt by small species. Anthropogenic activity reduced large herbivores biomass by 57%, estimated now at 82 Mt; consequently, small herbivores now dominate global herbivore biomass with 98 Mt (-29%). Losses vary greatly across climatic zones and functional groups, suggesting that size is not the only discriminant feature of biomass decline. Actual evapotranspiration is the most important driver of total, large, and small herbivore biomass and explains 64%, 59%, and 49% of its variation, respectively. Energy and water dependency is high for large herbivores, whose biomass is greater in hot and wet areas, challenging the notion that large herbivore biomass peaks in savannas only. Outside Africa and the Tropics, potential-biomass hotspots occur in areas today dominated by humans; this could undermine the recovery of larger species in certain areas. These herbivore biomass estimates provide a quantitative benchmark for setting conservation and rewilding goals at large spatial scales. The herbivore model and functional classification create new opportunities to integrate mammals into Earth System science and models.

ecology↗

bioRxiv2021

Progressive chromatin silencing of ABA biosynthesis gene permits seed germination in Arabidopsis

Seed germination represents a major developmental switch in plants that is vital to agricultural, but how this process is controlled at the chromatin level remains obscure. Here we demonstrate that successful germination in Arabidopsis requires a chromatin mechanism that progressively silences NCED6, which encodes a rate-limiting enzyme for abscisic acid (ABA) biosynthesis, through the cooperative action of the RNA-binding protein RZ-1 and the polycomb repressive complex 2 (PRC2). Simultaneous inactivation of RZ-1 and PRC2 blocks germination and synergistically derepresses NCEDs and hundreds of genes. At NCED6, by promoting H3 deacetylation and suppressing H3K4me3, RZ-1 facilitates transcriptional silencing and also a H3K27me3 accumulation process that occurs during seed germination and early seedling growth. Genome-wide analysis reveals RZ-1 is preferentially required for transcriptional silencing of many PRC2 targets early during seed germination when H3K27me3 is not yet established. We propose RZ-1 confers a novel silencing mechanism to compensate and coordinate with PRC2. Our work highlights the progressive chromatin silencing of ABA biosynthesis genes via synergized action of the RNA-binding protein RZ1 and PRC2, which is vital for seed germination.

plant biology↗

bioRxiv2021

Solid optical clearing agents based through-Intact-Skull (TIS) window technique for long-term observation of cortical structure and function in mice

In vivo cortical optical imaging needs to overcome the scattering of skull. Compared to the traditional transcranial surgery-based open-skull glass window and thinned-skull preparation, chemical tissue optical clearing techniques can provide a skull-remained optical access to the brain while maintaining its original environment. However, previously demonstrated skull optical clearing windows could only maintain transparency for a couple of hours and hardly capable for high-resolution monitoring of awake animals. Here, we developed a convenient and easy-handling chronic skull optical clearing technique, named "Through-Intact-Skull (TIS) window", which was compatible with long-term observation at high resolution, and yielded large imaging depth of 900 m for cortical neurovascular visualization. In addition, our TIS window could monitor neuron activity in awake mice for a long term. Therefore, our bio-compatible and non-invasive TIS window is a new promising approach for intravital brain microscopy with great potential for basic research in neuroscience.

neuroscience↗

bioRxiv2021

Ultrafast, one-step, and microwave heating-based synthesis of DNA/RNA-AuNP conjugates

DNA/RNA-gold nanoparticle (DNA/RNA-AuNP) nanoprobes have been widely employed for nanobiotechnology applications. Here we discovered that both thiolated and non-thiolated DNA/RNA can be efficiently attached to AuNPs to achieve high-stable spherical nucleic acid (SNA) within minutes under a domestic microwave (MW)-assisted heating-dry circumstance. Further studies showed that for non-thiolated DNA/RNA the conjugation is poly (T/U) tag dependent. Spectroscopy, test strip hybridization, and loading counting experiments indicate that low-affinity poly (T/U) tag mediates the formation of a standing-up conformation, which is distributed in the outer layer of such a SNA structure. In further applications study, CRISPR/Cas9-sgRNA (135 bp), RNA from Nucleocapsid (N) gene of SARS-CoV-2 (1279 bp), and rolling circle amplification (RCA) DNA products (over 1000 bp) could be successfully attached on AuNPs, which overcomes the routine methods in long-chain nucleic acid-AuNP conjugation, exhibiting great promise in novel biosensing and nucleic acids delivery strategy. This novel heating-dry strategy has improved the traditional DNA/RNA-AuNP conjugation methods in simplicity, rapidity, cost, and universality.

biochemistry↗

bioRxiv2021

Iron promotes Slc7a11-deficient valvular interstitial cell osteogenic differentiation: A possible mechanism by which ferroptosis participates in intraleaflet hemorrhage-induced calcification.

BackgroundCalcific aortic valve disease (CAVD) is the most frequent pathogeny of aortic valve replacement in developed countries. Iron deposits are found in the intraleaflet hemorrhage (IH) areas of calcific aortic valves. Ferroptosis is a form of regulated cell death that involves metabolic dysfunction resulting from iron overload-dependent excessive lipid peroxidation. In this research, we attempted to clarify the role of ferroptosis in CAVD. MethodsThe level of ferroptosis in tissue and valvular interstitial cells (VICs) was assessed by the contents of 4-HNE, NADPH, ROS, and GSH, lipid peroxidation and mitochondrial morphology. The levels of calcification, iron accumulation and Slc7a11 expression in surgical aortic valve specimens were detected by Alizarin red or Von Kossa, Perls blue and immunohistochemical staining. The osteogenic differentiation of VICs was assessed by PCR and western blot analyses. Furthermore, RNA sequencing was used to detect potential differentially expressed genes between normal and osteogenic medium-treated (OM-treated) VICs. ResultsOur experiments demonstrated that ferroptosis occurred in the IH areas of calcific aortic valves. We also found that Slc7a11 was expressed at low levels in OM-treated VICs and IH areas. Finally, we demonstrated that iron promoted Slc7a11-deficient VICs osteogenic differentiation by aggravating ferroptosis in vitro. ConclusionIn conclusion, iron promotes Slc7a11-deficient VIC osteogenic differentiation by aggravating ferroptosis in vitro, thereby accelerating the progression of aortic valve calcification. StatementStatements and opinions expressed in the articles and communications herein are those of the author(s) and not necessarily those of the Editor(s), Society, or publisher, and the Editor(s), Society, and publisher disclaim any responsibility or liability for such material. Brief SummaryIn this work, two novel notions have been proposed. First, we reported that ferroptosis participated in the progression of CAVD. Second, this is the first cytology experiment of valvular interstitial cells (VICs) to clarify the mechanism by which intraleaflet hemorrhage aggravates calve calcification. This research provides new ideas and targets for alleviating the progression of CAVD, especially in patients who have calcified aortic valves without severe stenosis.

molecular biology↗

bioRxiv2021

Genetic loci of the R. anatipestifer serotype discovered by Pan-GWAS and its application for the development of a multiplex PCR serotyping method

The disease caused by Riemerella anatipestifer (R. anatipestifer) causes large economic losses to the global duck industry every year. Serotype-related genomic variation (such as in O-antigen and capsular polysaccharide gene clusters) has been widely used for the serotyping in many gram-negative bacteria. To date, there have been few studies focused on genetic basis of serotypes in R. anatipestifer. Here, we used pan-genome-wide association studies (Pan-GWAS) to identify the serotype-specific genetic loci of 38 R. anatipestifers strain. Analyses of the loci of 11 serotypes showed that the loci could be well mapped with the serotypes of the corresponding strains. We constructed the knockout strain for the wzy gene at the locus, and the results showed that the mutant lost the agglutination characteristics to positive antisera. Based on the of Pan-GWAS results, we developed a multiple PCR method to identify serotypes 1, 2, and 11 of R. anatipestifer. Our study provides a precedent for systematically analysing the genetic basis of the R anatipestifer serotypes and establishing a complete serotyping system in the future. HighlightsO_LIR. anatipestifer serotype-specific locus was identified by Pan-GWAS for the first time. C_LIO_LIMolecular serotyping multiplex PCR was developed based on O-antigen biosynthesis gene clusters C_LI

genomics↗

bioRxiv2021

VAL1 as an assembly platform co-ordinating co-transcriptional repression and chromatin regulation at Arabidopsis FLC

Polycomb (PcG) silencing is crucial for development across eukaryotes, but how PcG targets are regulated is still incompletely understood. The slow timescale of cold-induced PcG silencing at Arabidopsis thaliana FLOWERING LOCUS C (FLC) makes it an excellent system to dissect this mechanism. Binding of the DNA binding protein VAL1 to an FLC intronic RY motif within the PcG nucleation region is an early step in the silencing process. VAL1 interacts with APOPTOSIS AND SPLICING ASSOCIATED PROTEIN (ASAP) complex and POLYCOMB REPRESSIVE COMPLEX 1 (PRC1). Here, we show that ASAP and PRC1 function as co-repressors that quantitatively regulate FLC transcription. Upon the shift to cold PRC1-mediated H2Aub accumulates only at the nucleation region, is transiently maintained after transfer back to warm, but unlike the PRC2-delivered H3K27me3 does not spread across the locus. H2K27me3 thus provides long-term epigenetic silencing, whereas H2Aub is a transient repression signal. Overall, our work highlights how a DNA sequence-specific binding protein can act as an assembly platform co-ordinating the co-transcriptional repression and chromatin regulation necessary for Polycomb silencing.

molecular biology↗

bioRxiv2021

Atp13a5 Marker Reveals Pericytes of The Central Nervous System in Mice

Perivascular mural cells including vascular smooth cells (VSMCs) and pericytes are integral components of the vascular system. In the central nervous system (CNS), pericytes are also known as the guardian of the blood-brain barrier, blood-spinal cord barrier and blood-retinal barrier, and play key roles in maintaining cerebrovascular and neuronal functions. However, the functional difference between CNS and peripheral pericytes has not been resolved at the genetic and molecular levels. Hence, the generation of reliable CNS pericyte-specific models and genetic tools remains very challenging. Here, we report a new CNS pericyte marker in mice. This cation-transporting ATPase 13A5 (Atp13a5) marker is highly specific to the pericytes in brain, spinal cord and retina. We generated a transgenic model with a knock-in tdTomato reporter and Cre recombinase. The tdTomato reporter reliably labels the CNS pericytes, but not found in any other CNS cell types including closely related VSMCs, or in peripheral organs. More importantly, Atp13a5 is turned on at embryonic day E15, suggesting brain pericytes are shaped by the developing neural environment. We hope that the new tools will allow us to further explore the heterogeneity of pericytes and achieve a better understanding of CNS pericytes in health and diseases.

neuroscience↗

bioRxiv2021

Exosomes from adipose-derived stem cells alleviate myocardial infarction via microRNA-31/FIH1/HIF-1α pathway

Our previous study has revealed that exosomes from adipose-derived stem cells (ASCs) promote angiogenesis in subcutaneously transplanted gels by delivery of microRNA-31 (miR-31) which targets factor inhibiting hypoxia-inducible factor-1 (FIH1) in recipient cells. Here we hypothesized that ASC exosomes alleviate ischemic diseases through miR-31/FIH1/hypoxia-inducible factor-1 (HIF-1) signaling pathway. Exosomes from ASCs were isolated by sequential centrifugations, and were characterized with nanoparticle tracking analysis, transmission electron microscopy, and immunoblotting analysis for exosomal markers. Results from laser imaging of ischemic mouse hindlimb revealed that exosomes enhanced the blood perfusion, and this enhancement was impaired when using miR-31-depleted exosomes. Immunohistochemistry analysis showed that administration of exosomes resulted in a higher arteriole density and larger CD31+ area in ischemic hindlimb than miR-31-delpleted exosomes. Similarly, knockdown of miR-31 in exosomes reduced the effects of the exosomes on increasing ventricular fraction shortening and CD31+ area, and on decreasing infarct size. Exosomes promoted endothelial cell migration and tube formation. These changes were attenuated when miR-31 was depleted in the exosomes or when FIH1 was overexpressed in the endothelial cells. Furthermore, the results from co-immunoprecipitation and luciferase reporter assay demonstrated that the effects of exosomes on elevating the binding of HIF-1 with co-activator p300 and enhancing HIF-1 activity were decreased when miR-31 was depleted in the exosomes or FIH1 was overexpressed. Our findings provide evidence that exosomes from ASCs promote angiogenesis in both mouse ischemic hindlimb and heart through transport of miR-31 which targets FIH1 and therefore triggers HIF-1 transcriptional activation.

molecular biology↗

bioRxiv2021

Effect of charge on protein preferred orientation at the air-water interface in cryo-electron microscopy

The air-water interface (AWI) tends to absorb proteins and frequently causes preferred orientation problems in cryo-electron microscopy (cryo-EM). Here, we examined cryo-EM data from protein samples frozen with different detergents and found that both anionic and cationic detergents promoted binding of proteins to the AWI. By contrast, nonionic and zwitterionic detergents tended to prevent proteins from attaching to the AWI. This ability was positively associated with the critical micelle concentration of the detergent. The protein orientation distributions with different anionic detergents were similar and resembled that obtained without detergent. By contrast, cationic detergents gave distinct orientation distributions. The AWI is negatively charged and the absorption of cationic detergents to the AWI alters its charge. Our results indicates that proteins absorb to charged interface and the negative charge of the AWI plays an important role in absorbing proteins in the conventional cryo-EM sample preparation. According to these findings, a new method was developed to modify the charge distribution of the AWI by adding a very low concentration of anionic detergent. Using this method, the protein particles exhibited a more evenly distributed orientations and still absorbed to the AWI enabling them embedding in a thin layer of ice, which will benefit the cryo-EM structural determination.

biophysics↗

bioRxiv2021

FliW and CsrA govern flagellin (FliC) synthesis and play pleiotropic roles in virulence and physiology of Clostridioides difficile R20291

Clostridioides difficile is a Gram-positive, spore-forming, and toxin-producing anaerobe that can cause nosocomial antibiotic-associated intestinal disease. In C. difficile, the expression of flagellar genes is coupled to toxin gene regulation and bacterial colonization and virulence. The flagellin FliC is responsible for pleiotropic gene regulation during in vivo infection. However, how fliC expression is regulated is unclear. In Bacillus subtilis, flagellin homeostasis and motility are coregulated by flagellar assembly factor FliW, Flagellin Hag (FliC homolog), and CsrA (Carbon storage regulator A), which is referred to as partner-switching mechanism "FliW-CsrA-Hag". In this study, we characterized FliW and CsrA functions by deleting or overexpressing fliW, csrA, and fliW-csrA in C. difficile R20291. We showed that both fliW deletion or csrA overexpression in R20291, and csrA complementation in R20291{Delta}WA (fliW-csrA codeletion) dramatically decreased FliC production, however, fliC gene transcription was unaffected. While suppression of fliC translation by csrA overexpression was mostly relieved when fliW was coexpressed, and no significant difference in FliC production was detected when only fliW was complemented in R20291{Delta}WA. Further, loss of fliW led to increased biofilm formation, cell adhesion, toxin production, and pathogenicity in a mouse model of C. difficile infection (CDI), while fliW-csrA codeletion decreased toxin production and mortality in vivo. Taken together, these data suggest that CsrA negatively modulates fliC expression and FliW indirectly affects fliC expression through inhibition of CsrA post-transcriptional regulation, which seems similar to the "FliW-CsrA-Hag" switch in B. subtilis. Our data also suggest that "FliW-CsrA-fliC/FliC" can regulate many facets of C. difficile R20291 pathogenicity. IMPORTANCEC. difficile flagellin FliC is associated with toxin gene expression, bacterial colonization and virulence, and is also involved in pleiotropic gene regulation during in vivo infection. However, how fliC expression is regulated remains unclear. In light of "FliW-CsrA-Hag" switch coregulation mechanism reported in B. subtilis, we showed that fliW and csrA play an important role in flagellin synthesis which affects C. difficile motility directly. Our data also suggest that FliW-CsrA-fliC/FliC" can regulate many facets of C. difficile R20291 pathogenicity. These findings further aid us in understanding the virulence regulation in C. difficile.

microbiology↗

bioRxiv2021

Atrx deletion impairs cGAS-STING signaling and increases response to radiation and oncolytic herpesvirus in sarcoma

ATRX is one of the most frequently altered genes in solid tumors, and mutation is especially frequent in soft tissue sarcomas. However, the role of ATRX in tumor development and response to cancer therapies remains poorly understood. Here, we developed a primary mouse model of soft tissue sarcoma and showed that Atrx deleted tumors are more sensitive to radiation therapy. In the absence of Atrx, irradiated sarcomas have increased persistent DNA damage, telomere dysfunction, and mitotic catastrophe. We find that Atrx deleted sarcomas have a reduced adaptive immune response, impaired cGAS-STING signaling, and increased sensitivity to an oncolytic herpesvirus therapy. Translation of these results to patients with ATRX mutant cancers could enable genomically-guided cancer therapeutic approaches that improve patient outcomes.

cancer biology↗

bioRxiv2021

ZFP207 controls pluripotency by multiple post-transcriptional mechanisms

The pluripotent state is not solely governed by the action of the core transcription factors Oct4, Sox2, and Nanog, but also by a series of co-transcriptional and post-transcriptional events, including alternative splicing (AS) and the interaction of RNA-binding proteins (RBPs) with defined subpopulations of RNAs. Zinc Finger Protein 207 (ZFP207) is an essential transcription factor for mammalian embryonic development. Here, we employ multiple functional analyses to characterize the role of ZFP207 in mouse embryonic stem cells (ESCs). We find that ZFP207 plays a pivotal role in ESC maintenance, and silencing of Zfp207 leads to severe neuroectodermal differentiation defects. In striking contrast to human ESCs, ZFP207 does not transcriptionally regulate stem cell and neuronal-related genes but exerts its effects by control AS networks and acting as an RBP. Our study expands the role of ZFP207 to maintain ESC identity, and underscores ZFP207 functional versatility with key roles in neural fate commitment.

cell biology↗

bioRxiv2021

Structural and molecular basis for foot-and-mouth disease virus neutralization by two potent protective antibodies

Outbreaks of Foot-and-mouth disease (FMD) caused by FMD virus result in significant economic losses. Vaccination is helpful, but the benefits are diminished with antigenic diversity within serotypes, instability of the immunogen and inability to confer protection for long durations. Here we have further dissected the mechanisms underpinning the protective efficacy of two previously reported neutralizing antibodies (NAbs), M8 and M170. The atomic details of the epitopes of M8 and M170 unveiled suggest that protection is conferred by disrupting the virus-receptor interactions. Consequently, administration of these NAbs conferred prophylactic and therapeutic benefit in guinea pigs, raising the possibility of administering NAbs before or during vaccination to confer immediate protection; well before the bolstering of the immune response by the vaccine. Differences in the residues and the conformation of elements making up the epitopes explain the differences in specificities of M8 and M170. An ability to bind 146S viral particles specifically, but not 12S degraded components, highlights a likely role for M170 in the quality control of vaccines.

biophysics↗

bioRxiv2020

Evaluation of exosome-encapsulated miR-23a/b in the diagnosis of human coronary heart diseases

ObjectiveCoronary heart disease (CHD) is currently one of the major causes of death with high morbidity. Due to the increasing heterogeneity and complexity in the CHDs progression, biomarkers for specific diagnosis and monitoring of disease progression need to be developed. The study was aimed to investigate the roles of serum exosomal miR-23a and miR-23b in diagnosis of CHDs. Methods16 healthy individuals and 56 patients with CHDs were enrolled in this study, including the CHDs of stable angina, unstable angina, non-ST elevation myocardial infarction (NSTEMI), ST elevation myocardial infarction (STEMI) and acute myocardial infarction (AMI). Serum exosomal miR-23a and miR-23b were quantified by Q-PCR. The associations of miR-23a/b with multiple clinical parameters were analyzed. ResultsSerum exosomal miR-23a was downregulated in the 56 CHD patients. In the specific prediction of stable angina and AMI, miR-23a achieved the area under the receiver operating characteristic (AUC-ROC) of 0.809 and 0.783, respectively. The levels of serum creatinine (CREA) and miR-23a were associated, which was consistent with risk of kidney injury in CHDs patients. Exosomal miR-23b levels showed no difference among CHD groups. ConclusionsmiR-23a may serve as a non-invasive marker in predicting stable angina and AMI. The level of miR-23a was implicated in CREA-dependent CHD-renal damage.

pathology↗

bioRxiv2020

Longest Order Conserved Exemplar Subsequences

We propose a new problem whose input data are two linear genomes together with two indexed gene subsequences of them, which asks to find a longest common exemplar subsequence of the two given genomes with a subsequence identical to the given indexed gene subsequences. We present an algorithm for this problem such that the algorithm is allowed to take diminishing time and space to solve the problem by setting the indexed genes with an incremental number. Although an incremental number of indexed genes were selected, the algorithm was verified definite to reach a solution whose length insistently comes very close to a real longest common exemplar subsequence of the two given genomes. Aiming at 23 human/gorilla chromosome pairs, the algorithm was examined for use in questing for longest common exemplar subsequences whose basic units are annotated genes as well as pseudo genes, namely consecutive DNA subsequences. By contrasting the pseudo gene common exemplar subsequences the algorithm had reached for the human chromosomes 7 and 16 and their gorilla homologues with those annotated genes in the human and gorilla chromosomes, we found more than 1 000 and 500 pseudo genes in the human chromosomes 7 and 16 that occur in the same order as they are in the gorilla chromosomes 7 and 16 and, do not overlap with any annotated gene. Author summaryThere is a benefit of the algorithm: It can reach a long enough common exemplar subsequence of two linear genomes in as fast a speed as one requires even if the given genomes would be equipped with too many duplicated genes, which can be done by setting incremental number of indexed genes. We developed a Java software based on the algorithm, that has been available for download on https://github.com/ShuZhang-sdu/LCES. Only in need to set the indexed gene sequences as null, was it verified successful for our algorithm to obtain the longest common exemplar subsequences of the annotated gene summary pairs extracted from 23 human/gorilla chromosome pairs. In convenience for researchers to find new motifs or conserved genes, we devoted for the algorithm to quest pseudo gene (i.e. consecutive DNA subsequences) summary pairs of the 23 human/gorilla chromosome pairs for solutions. There are 20 pseudo gene summary pairs whose longest common exemplar subsequences have been found by the algorithm with null indexed gene sequences. The other 3 pseudo gene summary pairs were verified solvable for the algorithm to reach their longest common exemplar subsequences that have to admit subsequences identical to given indexed gene subsequences. There were informed to exist 2 353 and 1 148 pseudo genes in the gorilla chromosome 7 and 16 that occur in the same order as they are in the human chromosome 7 and 16 and, do not overlap with any annotated gene. These pseudo genes should be significant for annotating the human or gorilla genome.

bioinformatics↗