Biology subjects

Xia, X.

Publications and source records attributed to Xia, X..

At least 91 records · Page 5Linked to original sources

bioRxiv2021

Simultaneous Cardiac and Neurological Monitoring to Assess Chemical Exposures and Drug Toxicity in Xenopus Laevis

Simultaneous monitoring of electrocardiogram (ECG) and electroencephalogram (EEG) under chemical exposure requires innovative engineering techniques that can capture minute physiological changes in studied animal models. However, this is often administered with a bulky system that may cause signal distortions and discomfort for animals. We develop an integrated bioelectronic sensing system to provide simultaneous ECG and EEG assessment in real-time under chemical exposure for Xenopus laevis. The microelectrode array (MEA) membrane with integrated ECG and EEG sensing offers an opportunity to achieve multichannel noninvasive electrophysiological monitoring with favorable dimensions and spatial resolution. To validate the performance of our system, we assessed the ECG and EEG of Xenopus under exposure of Pentylenetetrazol (PTZ), an epilepsy-inducing drug. Effects of PTZ were detected with clear ECG and EEG alterations, including frequent ictal and interictal EEG events, 30 dB average EEG amplitude elevations, abnormal ECG morphology, and heart rate changes. Overall, our Xenopus-based real-time electrophysiology monitoring system holds high potential for many applications in drug screening and remote environmental toxicity monitoring.

physiology↗

bioRxiv2021

Structure-based screening of drug candidates targeting the SARS-CoV-2 envelope protein

The COVID-19 (coronavirus disease 2019) pandemic is caused by SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2). SARS-CoV-2 produces a small hydrophobic envelope (E) protein which shares high homology with SARS-CoV E protein. By patch-clamp recording, the E protein is demonstrated to be a cation-selective ion channel. Furthermore, the SARS-CoV-2 E protein can be blocked by a SARS-CoV E protein inhibitor hexamethylene amiloride. Using structural model and virtual screening, another E protein inhibitor AZD5153 is discovered. AZD5153 is a bromodomain protein 4 inhibitor against hematologic malignancies in clinical trial. The E protein amino acids Phe23 and Val29 are key determinants for AZD5153 sensitivity. This study provides two promising lead compounds and a functional assay of SARS-CoV-2 E protein for the future drug candidate discovery.

biophysics↗

bioRxiv2021

A bacterium-like particle vaccine displaying Zika virus prM-E induces systemic immune responses in mice

The emergence of Zika virus (ZIKV) infection, which is an unexpectedly associated with congenital defects, has prompted the development of safe and effective vaccines. The gram-positive enhancer matrix-protein anchor (GEM-PA) display system has emerged as a versatile and highly effective platform for delivering target proteins for vaccines. In this article, we developed a bacterium-like particle vaccine ZI-{Delta}-PA-GEM based on the GEM-PA system. The fusion protein ZI-{Delta}-PA, which contains the prM-E-{Delta} protein of ZIKV (with a stem-transmembrane region deletion) and the protein anchor PA3, was expressed. The fusion protein was successfully displayed on the GEM surface, forming ZI-{Delta}-PA-GEM. Moreover, when BALB/c mice were immunized intramuscularly with ZI-{Delta}-PA-GEM combined with 201 VG and poly(I:C) adjuvants, durable ZIKV-specific IgG and protective neutralizing antibody responses were induced. Potent B cell/DC activation was also be stimulated early after immunization. Remarkably, splenocyte proliferation, the secretion of multiple cytokines, T/B cell activation and central memory T cell responses were elicited. These data indicate that ZI-{Delta}-PA-GEM is a promising bacterium-like particle vaccine candidate for ZIKV. Author summaryBecause Zika virus (ZIKV) infection is considered as an example of "disease X", the development of a safe and effective ZIKV vaccine is essential. The gram-positive enhancer matrix-protein anchor (GEM-PA) display system has been used in many vaccine studies due to its advantages. In this study, prM-E-{bigtriangleup} protein of ZIKV (with a stem-transmembrane region deletion) and the protein anchor PA3 was fusion expressed, termed ZI-{bigtriangleup}-PA. Then the fusion protein ZI-{bigtriangleup}-PA could be displayed on the surface of GEM, forming ZI-{bigtriangleup}-PA-GEM. The author evaluated the immunogenicity of ZI-{bigtriangleup}-PA-GEM with the 201 VG and poly(I:C) adjuvants. The study demonstrates that ZI-{bigtriangleup}-PA-GEM induced mice to produce neutralizing antibody and specific cellular immune responses. The author believe that the bacterium-like particle vaccine ZI-{bigtriangleup}-PA-GEM has the potential to be used as the ZIKV vaccine.

microbiology↗

bioRxiv2021

A new single-cell level R-index for EGFR-TKI resistance and survival prediction in LUAD

EGFR-TKIs achieved excellent efficacy in EGFR-mutated patients. Unfortunately, most patients would inevitably develop progressive disease within a median of 10 to 14 months. Predicting the resistance probability remains a challenge. Therefore, we created an R-index model trained by single-cell RNA data with the OCLR algorithm. This model can be applied to estimate the level of EGFR-TKI resistance in cell line and xenograft mice models and predict prognosis in multiple cohorts. Comparing the high and the low R-index group, we found that the glycolysis pathway and KRAS up-regulation pathway were related to resistance, and MDSC was the leading cause of immunosuppression in the tumor microenvironment. These results are consistent with previous studies indicating that the R-index provides an insight into resistance status and a new way to explore resistance mechanisms and clinical treatment by the combination of Glucose metabolism-targeted or MDSC-targeted therapies. This is the first quantification method of EGFR-TKI resistance based on single-cell sequencing data solving the problem of the mixed resistance state of tumor cells and helping explore transcriptome characteristics of drug-resistant cell populations.

bioinformatics↗

bioRxiv2021

Alpha oscillatory activity causally linked to working memory retention: insights from online phase-locking closed-loop transcranial alternating current stimulation (tACS)

Although previous studies have reported correlations between alpha oscillations and the "retention" sub-process of working memory (WM), causal evidence has been limited in human neuroscience due to the lack of delicate modulation of human brain. Conventional tACS is not suitable for demonstrating the causal evidence for parietal alpha oscillations in WM retention because of its inability to modulate brain oscillations within a short period (i.e., the retention sub-process). Here, we developed an online phase-corrected closed-loop transcranial alternating current stimulation (tACS) system capable of precisely correcting for the phase differences between tACS and concurrent endogenous oscillations. This system permits both up- and down-regulation of brain oscillations at the target stimulation frequency within a short stimulation period, and is here applied to empirically demonstrate that parietal alpha oscillations causally relate to WM retention. Our experimental design included both in-phase and anti-phase alpha-tACS applied to 39 participants during the retention sub-processes of a modified Sternberg paradigm. Compared to in-phase alpha-tACS, anti-phase alpha-tACS decreased both WM performance and alpha activity. Moreover, the in-phase tACS-induced changes in WM performance were positively correlated with alpha oscillatory activity. These findings strongly support a causal link between alpha oscillations and WM retention, and illustrate the broad application prospects of phase-corrected tACS.

neuroscience↗

bioRxiv2021

High Gamma and Beta Temporal Interference Stimulation in the Human Motor Cortex Improves Motor Functions

BackgroundTemporal interference (TI) stimulation is a new technique of noninvasive brain stimulation. Envelope-modulated waveforms with two high-frequency carriers can activate neurons in target brain regions without stimulating the overlying cortex, which has been validated in mouse brains. However, whether TI stimulation can work on the human brain has not been elucidate. ObjectiveTo assess the effectiveness and safety aspect of the envelope-modulated waveform of TI stimulation on human primary motor cortex (M1). MethodsParticipants attended three sessions of 30-min TI stimulation at 2 mA during a random reaction time task (RRTT) or a serial reaction time task (SRTT). Motor cortex excitability was measured before and after TI stimulation. ResultsIn the RRTT experiment, only 70 Hz TI stimulation had a promoting effect on the reaction time (RT) performance and excitability of the motor cortex compared to sham stimulation. Meanwhile, compared with the sham condition, only 20 Hz TI stimulation significantly facilitated motor learning in the SRTT experiment, which was significantly positively correlated with the increase in motor evoked potential. ConclusionThese results indicate that the envelope-modulated waveform of TI stimulation has a significant promoting effect on human motor functions, experimentally suggesting the effectiveness of TI stimulation in humans for the first time and pave the way for further explorations.

neuroscience↗

bioRxiv2021

Development of a Triazolobenzodiazepine-Based PET Probe for Subtype-Selective Vasopressin 1A Receptor Imaging

ObjectivesTo enable non-invasive real-time quantification of vasopressin 1A (V1A) receptors in peripheral organs, we sought to develop a suitable PET probe that would allow specific and selective V1A receptor imaging in vitro and in vivo. MethodsWe synthesized a high-affinity and -selectivity ligand, designated compound 17. The target structure was labeled with carbon-11 and tested for its utility as a V1A-targeted PET tracer by cell uptake studies, autoradiography, in vivo PET imaging and ex vivo biodistribution experiments. ResultsCompound 17 (PF-184563) and the respective precursor for radiolabeling were synthesized in an overall yield of 49% (over 7 steps) and 40% (over 8 steps), respectively. An inhibitory constant of 0.9 nM towards the V1A receptor was measured, while excellent selectivity over the related V1B, V2 and OT receptor (IC50 >10,000 nM) were obtained. Cell uptake studies revealed considerable V1A binding, which was significantly reduced in the presence of V1A antagonists. Conversely, there was no significant blockade in the presence of V1B and V2 antagonists. In vitro autoradiography and PET imaging studies in rodents indicated specific tracer binding mainly in the liver. Further, the pancreas, spleen and the heart exhibited specific binding of [11C]17 ([11C]PF-184563) by ex vivo biodistribution experiments. ConclusionWe have developed the first V1A-targeted PET ligand that is suitable for subtype-selective receptor imaging in peripheral organs including the liver, heart, pancreas and spleen. Our findings suggest that [11C]PF-184563 can be a valuable tool to study the role of V1A receptors in liver diseases, as well as in cardiovascular pathologies.

pharmacology and toxicology↗

bioRxiv2021

Pixelwise H-score: a novel digital image analysis based-metric to quantify membrane biomarker expression from immunohistochemistry images

Immunohistochemistry (IHC) assays play a central role in evaluating biomarker expression in tissue sections for diagnostic and research applications. Manual scoring of IHC images, which is the current standard of practice, is known to have several shortcomings in terms of reproducibility and scalability to large scale studies. Here, by using a digital image analysis-based approach, we introduce a new metric called the pixelwise H-score (pix H-score) that quantifies biomarker expression from whole-slide scanned IHC images. The pix H-score is an unsupervised algorithm that only requires the specification of intensity thresholds for the biomarker and the nuclear-counterstain channels. We present the detailed implementation of the pix H-score in two different whole-slide image analysis software packages Visiopharm and HALO. We consider three biomarkers P-cadherin, PD-L1, and 5T4, and show how the pix H-score exhibits tight concordance to multiple orthogonal measurements of biomarker abundance such as the biomarker mRNA transcript and the pathologist H-score. We also compare the pix H-score to existing automated image analysis algorithms and demonstrate that the pix H-score provides either comparable or significantly better performance over these methodologies. We also present results of an empirical resampling approach to assess the performance of the pix H-score in estimating biomarker abundance from select regions within the tumor tissue relative to the whole tumor resection. We anticipate that the new metric will be broadly applicable to quantify biomarker expression from a wide variety of IHC images. Moreover, these results underscore the benefit of digital image analysis-based approaches which offer an objective, reproducible, and highly scalable strategy to quantitatively analyze IHC images.

pathology↗

bioRxiv2020

Response of methanogen community to elevation of cathode potentials in the presence of magnetite

Electromethanogenesis refers to the process where methanogens utilize electrons derived from cathodes for the reduction of CO2 to CH4. Setting of low cathode potentials is essential for this process. In this study, we test if magnetite, an iron oxide mineral widespread in environment, can facilitate the adaption of methanogen community to the elevation of cathode potentials in electrochemical reactors. Two-chamber electrochemical reactors were constructed with inoculants obtained from a paddy field soil. We elevated cathode potentials stepwise from the initial -0.6 V vs standard hydrogen electrode (SHE) to -0.5 V and then to -0.4 V over the 120 days acclimation. Only weak current consumption and CH4 production were observed in the reactors without magnetite. But biocathodes were firmly developed and significant current consumption and CH4 production were recorded in the magnetite reactors. The robustness of electro-activity in the magnetite reactors was not affected with the elevation of cathode potentials from -0.6 V to -0.4 V. But, the current consumption and CH4 production were virtually halted in the reactors without magnetite when cathode potential was elevated to -0.4 V. Methanogens related to Methanospirillum were enriched on cathode surface of the magnetite reactors at -0.4 V, while Methanosarcina relatively dominated in the reactors without magnetite. Methanobacterium also increased in the magnetite reactors but stayed off electrodes in the culture medium at -0.4 V. Apparently, magnetite greatly facilitates the development of biocathodes, and it appears that with the aid of magnetite Methanospirillum spp. can adapt to high cathode potentials performing the efficient electromethanogenesis. IMPORTANCEConverting CO2 to CH4 through bioelectrochemistry is a promising approach for development of green energy biotechnology. This process however requires setting the low cathode potentials, which takes cost. In this study, we test if magnetite, a conductive iron mineral, can facilitate the adaption of methanogens to the elevation of cathode potentials. In the two-chamber reactors constructed using inoculants obtained from a paddy field soil, biocathodes were firmly developed in the presence of magnetite, whereas only weak electro-activity was observed in the reactors without magnetite. The elevation of cathode potentials did not affect the robustness of electro-activity in the magnetite reactors over the 120 days acclimation. Methanospirillum was identified as the key methanogens associated with cathode surface during the operation at relatively high potentials. The findings reported in this study shed a new light on the adaption of methanogen community to the elevated cathode potentials in the presence of magnetite.

bioengineering↗

bioRxiv2020

Nav1.3 and fibroblast growth factor homologous factor 14 are primary determinants of the TTX-sensitive sodium current in mouse adrenal chromaffin cells

Adrenal chromaffin cells (CCs) in rodents express a rapidly inactivating, TTX-sensitive sodium current. The current has generally been attributed to Nav1.7, although a possible role for Nav1.3 has also been suggested. Nav channels in rat CCs rapidly inactivate into two separable pathways, which differ in their time course of recovery from inactivation. One population recovers with time constants similar to traditional fast inactivation and the other about 10-fold slower. Inactivation properties suggest that the two pathways result from a single homogenous population of channels. Here we probe the properties and molecular components of the Nav current present in mouse CCs. We first confirm that functional properties of Nav current in rat and mouse cells are generally similar in terms of activation range, steady-state inactivation, and dual pathway fast inactivation. The results then show that all inward Nav current is absent in CCs from Nav1.3 KO mice. Subsequently, in a mouse with KO of fibroblast growth factor homology factor 14 (FGF14), we find that the slow component of recovery from fast inactivation is completely absent in most CCs, with no change in the time constant of fast recovery. Experiments probing the use-dependence of Nav current diminution between WT and FGF14 KO mice directly demonstrate a role of slow recovery from inactivation in determination of Nav current availability. Overall, the results indicate that the FGF14-mediated inactivation is the major determinant in defining use-dependent changes in Nav availability in CCs. We also consider the potential impact that inactivating FGFs with different recovery kinetics can exert on differential use-dependent changes in Nav availability.

biophysics↗

bioRxiv2020

Goblet cell LRRC26 regulates BK channel activation and protects against colitis in mice

Goblet cells (GCs) are specialized cells of the intestinal epithelium contributing critically to mucosal homeostasis. One of the functions of GCs is to produce and secrete MUC2, the mucin that forms the scaffold of the intestinal mucus layer coating the epithelium and separates the luminal pathogens and commensal microbiota from the host tissues. Although a variety of ion channels and transporters are thought to impact on MUC2 secretion, the specific cellular mechanisms that regulate GC function remain incompletely understood. Previously, we demonstrated that leucine-rich-repeat-containing protein 26 (LRRC26), a known regulatory subunit of the Ca2+-and voltage-activated K+ channel (BK channel), localizes specifically to secretory cells within the intestinal tract. Here, utilizing a mouse model in which MUC2 is fluorescently tagged allowing visualization of single GCs in intact colonic crypts, we show that murine colonic GCs have functional LRRC26-associated BK channels. In the absence of LRRC26, BK channels are present in GCs, but are not activated at physiological conditions. In contrast, all tested MUC2-negative cells completely lacked BK channels. Moreover, LRRC26-associated BK channels underlie the BK channel contribution to the resting transepithelial current across mouse distal colonic mucosa. Genetic ablation of either LRRC26 or BK-pore forming -subunit in mice results in a dramatically enhanced susceptibility to colitis induced by dextran sodium sulfate (DSS). These results demonstrate that normal potassium flux through LRRC26-associated BK channels in GCs has protective effects against colitis in mice. SignificanceA primary function of goblet cells (GCs) of the intestinal epithelium is to generate a protective mucus layer lining the intestinal lumen. GC dysfunction is linked to Inflammatory Bowel Disease (IBD). GC mucus secretion is thought to be dependent on contributions of an ensemble of anion and cation fluxes, although understanding remains limited. Here, it is shown in mouse colon that the Ca2+- and voltage-dependent BK-type K+ channel, specifically in association with the LRRC26 regulatory subunit, plays a critical role in normal GC function, protecting mice against chemically-induced colitis. The results demonstrate that normal K+ fluxes mediated by LRRC26-containing BK channels are required for normal GC function, potentially providing insights into the potential role of BK channels in IBD.

physiology↗

bioRxiv2020

Distinct mechanisms for TMPRSS2 expression explain organ-specific inhibition of SARS-CoV-2 infection by enzalutamide

The coronavirus disease 2019 (COVID-19) pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has rapidly become a global public health threat due to the lack of effective drugs or vaccines against SARS-CoV-2. The efficacy of several repurposed drugs has been evaluated in clinical trials. Among these drugs, a relatively new antiandrogen agent, enzalutamide, was proposed because it reduces the expression of transmembrane serine protease 2 (TMPRSS2), a key component mediating SARS-CoV-2-driven entry into host cells, in prostate cancer cells. However, definitive evidence for the therapeutic efficacy of enzalutamide in COVID-19 is lacking. Here, we evaluated the antiviral efficacy of enzalutamide in prostate cancer cells, lung cancer cells, human lung organoids and SARS-CoV-2-infected Ad-ACE2-transduced Tmprss2 knockout (Tmprss2-KO) and wild-type (WT) mice. TMPRSS2 knockout significantly inhibited SARS-CoV-2 infection in vivo. Enzalutamide effectively inhibited SARS-CoV-2 infection in human prostate cancer cells (LNCaP) but not in human lung cancer cells or patient-derived lung organoids. Although Tmprss2 knockout effectively blocked SARS-CoV-2 infection in ACE2-transduced mice, enzalutamide showed no antiviral activity due to the AR independence of TMPRSS2 expression in mouse and human lung epithelial cells. Moreover, we observed distinct AR binding patterns between prostate cells and lung cells and a lack of direct binding of AR to TMPRSS2 in human lung cells. Thus, our findings do not support the postulated protective role of enzalutamide in treating COVID-19.

microbiology↗

bioRxiv2020

Phylogenetic analysis by SNP and development of SSR marker in Passiflora

Information of the Passiflora genome is still very limited. Understand the evolutionary relationship between different species of Passiflora, and develop a large number of SSR markers to provide a basis for the genetic improvement of Passiflora. Applying restriction site associated DNA sequencing (RAD-Seq) technology, we studied the phylogeny, simple sequence repeat (SSR) and marker transferability of 10 accessions of 6 species of Passiflora. Taking the partial assembly sequence of accessions P4 as the reference genome, we constructed the phylogenetic tree using the detected 46,451 high-quality single nucleotide polymorphisms (SNPs), showing that P6, P7, P8 and P9 were a single one while P5 and P10 were clustered together, and P1, P2, P3 and P4 were closer in genetic relationship. Using P8 as the reference genome, a total of 12,452 high-quality SNPs were used to construct phylogenetic tree. P3, P4, P7, P8, P9 and P10 were all single branch while P1 and P2 were clustered together, and P5 and P6 were clustered into one branch. A principal component analysis (PCA) revealed a similar population structure, which four cultivated passion fruits forming a tight cluster. A total of 2,614 SSRs were identified in the genome of 10 Passiflora accessions. The core motifs were AT, GA, AAG etc., 2-6 bases, 4-16 repeats, and 2,515 pairs of SSR primer were successfully developed. Tthe SSR transferability in cultivated passion fruits is the best. These results will contribute to the study of genomics and molecular genetics in passion fruit.

molecular biology↗

bioRxiv2020

Berberine reverses multidrug resistance in Candida albicans by hijacking the drug efflux pump Mdr1p

Clinical use of antimicrobials faces great challenges from the emergence of multidrug resistant (MDR) pathogens. The overexpression of drug efflux pumps is one of the major contributors to MDR. It is considered as a promising approach to overcome MDR by reversing the function of drug efflux pumps. In the life-threatening fungal pathogen Candida albicans, the major facilitator superfamily (MFS) transporter Mdr1p can excrete many structurally unrelated antifungals, leading to multidrug resistance. Here we report a counterintuitive case of reversing multidrug resistance in C. albicans by using a natural product berberine to hijack the overexpressed Mdr1p for its own importation. Moreover, we illustrate that the imported berberine accumulates in mitochondria, and compromises the mitochondrial function by impairing mitochondrial membrane potential and mitochondrial Complex I. It results in the selective elimination of Mdr1p overexpressed C. albicans cells. Furthermore, we show that berberine treatment can prolong the mean survival time (MST) of mice with a blood-borne dissemination of Mdr1p overexpressed multidrug resistant candidiasis. This study provided a potential direction of novel anti-MDR drug discovery by screening for multidrug efflux pump converters.

microbiology↗

bioRxiv2020

Simple cloning of large natural product biosynthetic gene cluster by CRISPR/Cas12a-mediated fast direct capturing strategy

Directly cloning of biosynthetic gene clusters (BGCs) from microbial genomes has been revolutionizing the natural product-based drug discovery. However, it is still very challenging to efficiently clone, for example, large (> 80kb) and GC-rich (> 70%), streptomycete originating BGCs. In this study, we developed a simple, fast yet efficient and low-cost in vitro platform for direct cloning large BGCs from streptomycete genomic DNA, named as CAT-FISHING (CRISPR/Cas12a- and Agarose plug-based sysTem for Fast bIoSyntHetIc geNe cluster cloninG), by combining the advantages of CRISPR/Cas12a cleavage and bacterial artificial chromosome (BAC) library construction. CAT-FISHING was demonstrated by directly cloning large DNA fragments ranging from 47 to 139 kb with GC content of > 70% from the S. albus J1074 genome in a relatively efficient manner. Moreover, surugamides, encoded by a captured 87-kb BGC with GC content of 76%, was heterologously expressed in a Streptomyces chassis. These results indicate that CAT-FISHING is a powerful platform for BGCs batch cloning, which would be greatly beneficial to the natural products-based drug discovery. We believe that this system will lead a renaissance of interest in microorganisms as a source for drug development.

synthetic biology↗

bioRxiv2020

Coronavirus genomes carry the signatures of their habitats

Coronaviruses such as SARS-CoV-2 regularly infect host tissues that express antiviral proteins (AVPs) in abundance. Understanding how they evolve to adapt or evade host immune responses is important in the effort to control the spread of COVID-19. Two AVPs that may shape viral genomes are the zinc finger antiviral protein (ZAP) and the apolipoprotein B mRNA-editing enzyme-catalytic polypeptide-like 3 protein (APOBEC3). The former binds to CpG dinucleotides to facilitate the degradation of viral transcripts while the latter deaminates C into U residues leading to dysfunctional transcripts. We tested the hypothesis that both APOBEC3 and ZAP may act as primary selective pressures that shape the genome of an infecting coronavirus by considering a comprehensive number of publicly available genomes for seven coronaviruses (SARS-CoV-2, SARS-CoV, MERS, Bovine CoV, Murine MHV, Porcine HEV, and Canine CoV). We show that coronaviruses that regularly infect tissues with abundant AVPs have CpG-deficient and U-rich genomes; whereas viruses that do not infect tissues with abundant AVPs do not share these sequence hallmarks. In SARS-CoV-2, CpG is most deficient in the S protein region to evaded ZAP-mediated antiviral defense during cell entry. Furthermore, over four months of SARS-CoV-2 evolutionary history, we observed a marked increase in C to U substitutions in the 5 UTR and ORF1ab regions. This suggests that the two regions could be under constant C to U deamination by APOBEC3. The evolutionary pressures exerted by host immune systems onto viral genomes may motivate novel strategies for SARS-CoV-2 vaccine development.

bioinformatics↗

bioRxiv2020

Mapping Connectional Differences between Humans and Macaques in the Nucleus Accumbens Shell-Core Architecture

Two nucleus accumbens subregions, the shell and core, differ in the patterns whereby they integrate signals from prefrontal and limbic areas of the brain. In this study, we investigated whether the disproportionate volumetric differences of these brain areas, particularly the prefrontal cortex, between humans and macaques are accompanied by unique modifications of their macroscopic integrative connections with the shell and core. More specifically, we characterized the tractographic connectivity profiles of the human and macaque shell-core architecture and compared them between the two species. To make the cross-species comparisons more viable, we used the same whole-brain voxel-wise tractography-defined shell-like and core-like divisions in the two species as seeds and delineated pairs of interspecies connectionally comparable (ICC) target regions based on the similarity of the resting-state functional connectivity profiles for the two species, and finally used these seeds and ICC targets to establish a fingerprint-based common space for cross-species comparisons. Our results revealed that dissimilar structural connectivity profiles were found in the prefrontal but not the subcortical target group. We further localized this difference to specific targets to infer possible functional modifications between the two species.

neuroscience↗

bioRxiv2020

CRISPR-Assisted DNA Detection, a novel dCas9-based DNA detection technique

Nucleic acid detection techniques are always critical to diagnosis, especially in the background of the present COVID-19 pandemic. The simple and rapid detection techniques with high sensitivity and specificity are always urgently needed. However, the current nucleic acid detection techniques are still limited the traditional amplification and hybridization. To overcome the limitation, we here develop a CRISPR/Cas9-assisted DNA detection (CADD). In this detection, DNA sample is incubated with a pair of capture sgRNAs (sgRNAa and sgRNAb) specific to a target DNA, dCas9, a signal readout-related probe, and an oligo-coated solid support beads or microplate at room temperature for 15 min. During this incubation, the dCas9-sgRNA-DNA complex is formed and captured on solid support by the capture sequence of sgRNAa and the signal readout-related probe is captured by the capture sequence of sgRNAb. Finally the detection result is reported by a fluorescent or colorimetric signal readout. This detection was verified by detecting DNA of bacteria, cancer cell and virus. Especially, by designing a set of sgRNAs specific to 15 high-risk human papillomaviruses (HPVs), the HPV infection in 64 clinical cervical samples were successfully detected by the method. All detections can be finished in 30 minutes at room temperature. This detection holds promise for rapid on-the-spot detection or point-of-care testing (POCT).

biochemistry↗