Biology subjects

Jin, Z.

Publications and source records attributed to Jin, Z..

At least 73 records · Page 4Linked to original sources

bioRxiv2023

Sirenian genomes illuminate the evolution of fully aquatic species within the mammalian superorder Afrotheria

Sirenians of the diverse superorder Afrotheria were the first mammals to retransition from land to water and are the sole herbivorous marine mammals, but little is known about the underlying genomic changes. Here, we generated a chromosome-level dugong (Dugong dugon) genome. A comparison of our assembly and a recent West Indian manatee genome with other afrotherian genomes revealed possible molecular solutions to aquatic life by sirenians, including a shift in daily activity patterns (circadian clock) and tolerance to a high-iodine plant diet mediated through changes in the iodide transporter NIS (SLC5A5) and its co-transporters. Functional in vitro assays confirmed that sirenian amino acid substitutions alter the properties of the circadian clock protein PER2 and NIS. Sirenians show evidence of convergent regression of integumentary system (skin and its appendages) genes with cetaceans, the only other fully aquatic mammal group. Our analysis also uncovered gene losses that may be maladaptive in a modern environment, including a candidate gene (KCNK18) for sirenian cold stress syndrome likely lost during their evolutionary shift in daily activity patterns. Finally, genomes from nine Australian locations and the functionally extinct Okinawan population confirm and date a genetic break on the Australian east coast and highlight the need for whole-genome resequencing data from small or isolated dugong populations worldwide for conservation and genetic management.

evolutionary biology↗

bioRxiv2023

Neural signatures for temporal-order memory in the medial posterior parietal cortex

Episodic memory involves encoding and remembering the order of events experienced over time. Previous work examining the mechanisms of temporal-order memories has focused on the hippocampus and prefrontal cortices but has largely ignored the memory ensembles in the medial posterior parietal cortex (mPPC). Combining in vivo multi-unit electrophysiology and a temporal-order judgment task with cinematic material in the macaque, we find that mPPC neuronal activity reflects temporal context both during encoding and recall. During learning, mPPC neuronal ensembles encode the temporal information as well as contextual information embedded in the videos, whereas at retrieval these neurons fire in synchrony prior to memory-guided decisions. Moreover, the similarity between encoding and retrieval correlates with the animals performance. A control experiment further ruled out eye saccades, fixation, and scan path for their confounding roles in the neural results. Together, these data suggest that neurons in mPPC track the passage of time and contextual changes, thereby orchestrating for successful temporal-order memories at retrieval. SIGNIFICANCERemembering the temporal order of events is a vital function of the brain. This study provides the first evidence for the retrieval of temporal order of episodes at both single neuron and ensemble levels in the primate parietal cortex. The studys key breakthrough is the revelation that ensembles of time perceptive neurons, acting as "temporal context cells", can encode a spectrum of time constants and contexts for the experienced past and subsequently utilize this temporal record to discriminate the chronological order of past experiences. These results enhance theoretical frameworks for how encoded temporal past is maintained and reconstructed during memory retrieval.

neuroscience↗

bioRxiv2023

Well-ST-seq: cost-effective spatial transcriptomics at cellular level and high RNA capture efficiency

Spatial transcriptomic technologies are promising tools to reveal fine anatomical profiles of tissues. As for the methodologies based on barcoded probe arrays, improving the balance among probe barcoding complexity and cost, gene capture sensitivity, and spatial resolution can accelerate the spreading of spatial transcriptomic in basic science and clinical work. Here, based on miniaturized microfluidic and microarray technologies, we constructed a spatially cellular-level RNA-capture probe arrays. Owing to the predetermined and cost-effective probe fixation characteristics of the methodology, the consumable cost and fabrication time of the probe array can be reduced to $1.21/mm2 and approximately 2 hours, and the preparation process does not rely on large precision instruments. Moreover, the efficiency of the transcript captured by the probe array is even comparable to conventional single-cell RNA sequencing. Based on this technology, we achieved the spatial transcriptome expression mapping and gained insight into spatial cell heterogeneity of the mouse hippocampus.

genomics↗

bioRxiv2023

GABA, glucose and insulin orchestrate CD4+ T cells effector functions

Metabolic programs of immune cells are closely linked to their effector functions. Physiological molecules including glucose, insulin and {gamma}-aminobutyric acid (GABA) provide environmental cues and guidance, although how they coordinate to regulate the cells is still being unraveled. Here, we demonstrate that GABA-mediated reduction of metabolic activity and release of inflammatory molecules, including IFN{gamma} and IL-10, was abolished in human CD4+ T cells when the glucose concentration was elevated above normal levels. Insulin enhanced the GABAA receptors-mediated currents and Ca2+ influx. GABA decreased, whereas insulin sustained glycolysis but in a SGLT (Na+-glucose transporter)-dependent manner. In high glucose (16.7 mM), the SGLTs antagonist phlorizin alone or together with GABA restored the inhibition of IFN{gamma} and IL-10 release. This study exposes concerted effects of GABA, glucose and insulin on CD4+ T cells metabolic activity and release of inflammatory molecules, and identifies a role for SGLTs in CD4+ T cells function.

physiology↗

bioRxiv2023

Long-term reliable neural decoding based on flexible implantable microelectronics and machine learning for seizure prediction application

Neural decoding is useful for understanding brain functions and developing neural interface applications. However, neural interfaces based on rigid electronics often suffer from recording instability due to the foreign body responses caused by their mechanical mismatch with soft tissues, limiting the longitudinal accuracy of neural decoding methods. Herein, it is reported that flexible electronics can be integrated with machine learning algorithms to achieve long-term reliable neural decoding. Wet-spun conductive polymer microfibers showed mechanical robustness and flexibility, low impedance, and chronic biocompatibility, enabling intracerebral neural recordings in epileptic mice at a high signal-to-noise ratio eight weeks after implantation. When the signals recorded by the flexible electrodes were used in machine learning analyses with diverse complex algorithms, they consistently showed higher prediction accuracy for epileptic seizures than stiff metal electrode signals, particularly in the case of using long-term recordings for testing or small-sample datasets for training. A real-time warning system based on the flexible neural electrodes was built that predicted seizures eight minutes in advance with a low false alarm rate. Our work bridges flexible electronics and artificial intelligence for neural decoding applications such as long-term treatment of chronic neurological disorders.

bioengineering↗

bioRxiv2023

Aberration modeling in deep learning for volumetric reconstruction of light-field microscopy

Optical aberration is a crucial issue in optical microscopes, which fundamentally limits the practical imaging performance. As a commonly encountered one, spherical aberration is introduced by the refractive index mismatches between samples and environments, which will cause problems like low contrast, blurring, and distortion in imaging. Light-field microscopy (LFM) has recently emerged as a powerful tool for fast volumetric imaging. The appearance of spherical aberration in LFM will cause large changes of the point spread function (PSF) and thus greatly affects the imaging performance. Here, we propose the aberration-modeling view-channel-depth (AM-VCD) network for LFM reconstruction, which can well mitigate the influence of large spherical aberration. By quantitatively estimating the spherical aberration in advance and modeling it in the network training, the AM-VCD can obtain aberration-corrected high-speed visualization of three-dimensional (3D) processes with uniform spatial resolution and real-time reconstruction speed. Without any hardware modification, our method provides a convenient way to directly observe the 3D dynamics of samples in solution. We demonstrate the capability of AM-VCD under a large refractive index mismatch with volumetric imaging of a large-scale fishbone of largemouth bass. We further investigate the capability of AM-VCD in real-time volumetric imaging of dynamic zebrafish for tracking neutrophil migration.

bioengineering↗

bioRxiv2023

Magnetic Resonance Fingerprinting based Thermometry (MRFT): application to ex vivo imaging near DBS leads

The purpose of this study is to demonstrate the first work of T1-based magnetic resonance thermometry using magnetic resonance fingerprinting (dubbed MRFT). We compared temperature estimation of MRFT with proton resonance frequency shift (PRFS) thermometry on ex vivo bovine muscle. We demonstrated MRFTs feasibility in predicting temperature on ex vivo bovine muscles with deep brain stimulation (DBS) lead. B0 maps generated from MRFT were compared with gold standard B0 maps near the DBS lead. All experiments were performed on a 3 Tesla whole-body GE Premier system equipped with a 21-channel receive head coil (GE Healthcare, Milwaukee, WI). Four fluoroptic probes were used to measure the temperature at the center of a cold muscle (probe 1), the room temperature water bottle (probe 2), and the center and periphery of the heated muscle (probes 3 and 4). We selected regions of interest (ROIs) around the location of the probes and used simple linear regression to generate the temperature sensitivity calibration equations that convert T1 maps and {Delta}s maps to temperature maps. We then repeated the same setup and compared MRFT, PRFS thermometry temperature estimation with gold standard probe measurements. For the MRFT experiment on DBS lead, we taped the probe to the tip of the DBS lead and used a turbo spin echo (TSE) sequence to induce heating near the lead. We selected ROIs around the tip of the lead to compare MRFT temperature estimation with probe measurements. Vendor-supplied B0 mapping sequence was acquired to compare with MRFT-generated B0 maps. We found strong linear relationships (R2>0.958) between T1 and temperature and {Delta}s and temperatures in our temperature sensitivity calibration experiment. MRFT and PRFS thermometry both accurately predict temperature (RMSE<1.55 {degrees}C) compared to probe measurements. MRFT estimated temperature near DBS lead has a similar trend as the probe temperature. Both B0 maps show inhomogeneities around the lead.

bioengineering↗

bioRxiv2022

Heavy metal pollution characteristics of soil around a copper-nickel mine tailings pond in the northwest arid area of China and evaluation of desert phytoremediation potential

Phytoextraction and phytostabilization are two mechanisms used by plants to remove and stabilize heavy metals in soil. However, there has been little research on the extraction/stabilization of heavy metals by desert plants in arid areas. This study analyzed eight heavy metals (Cr, Ni, Cu, Zn, Cd, Pb, Mn, and As) in 10 desert plants and their growth matrices. In addition, the single factor pollution index and Nemerow comprehensive pollution index were used to evaluate soil pollution. Based on the biological accumulation factor and the biological concentration factor, the fuzzy evaluation method was used to evaluate plant extraction/stability potentials for heavy metals. The results showed that Cd, Cu, Ni, and Cr in the soil around the tailings pond were at the heavy pollution level, Mn and Pb pollution was moderate, and Zn and As pollution was light. The matrix factorization model showed that Cu and Ni came from industrial pollution; Cd and Cr came from atmospheric deposition and agricultural pollution; Pb came from traffic pollution; and Mn, Zn, and As came from natural sources. The metal contents of the desert plants exceeded the standard for normal plants, of which Cr contents in the Atriplex patens and Ammophila breviligulata Fernald aboveground parts were 35.63 and 53.77 mg/kg respectively, and the Ni contents in the Klasea centauroides subsp. polycephala (Iljin) L. Martins underground parts and the A. breviligulata Fernald aboveground parts were 102.67 and 101.67 mg/kg, respectively, exceeding the maximum toxicity threshold for Cr and Ni. Ammophila breviligulata Fernald had the highest plant comprehensive extraction coefficient (CEI) and plant comprehensive stability coefficient (CSI) at 0.81 and 0.83 respectively, indicating that it has strong heavy metal extraction and stabilization abilities. Therefore, A. breviligulata Fernald can be selected as a remediation species for heavy metal pollution in the soil around tailings reservoir areas.

ecology↗

bioRxiv2022

A di-arginine additive for dissociation of gold nanoparticle aggregates: A matrix-insensitive approach with applications in protease detection

We report the reversible aggregation of gold nanoparticle (AuNPs) assemblies via a diarginine peptide additive and thiolated PEGs (HS-PEGs). The AuNPs were first aggregated by attractive forces between the citrate-capped surface and the arginine side chains. We found that HS-PEG thiol group has higher affinity for the AuNPs surface, thus leading to redispersion and colloidal stability. In turn, there was a robust and obvious color change due to on/off plasmonic coupling. The assemblies dissociation was directly related to the HS-PEG structural properties such as their size or charge. As an example, HS-PEGs with a molecular weight below 1 kDa could dissociate 100% of the assemblies and restore the exact optical properties of the initial AuNPs suspension (prior to the assembly). Surprisingly, the dissociation capacity of HS-PEGs was not affected by the composition of the operating medium and could be performed in complex matrices such as plasma, saliva, bile, urine, cell lysates or even sea water. The high affinity of thiols for the gold surface encompasses by far the one of endogenous molecules and is thus favorized. Moreover, starting with AuNPs already aggregated ensured the absence of background signal as the dissociation of the assemblies was far from spontaneous. Remarkably, it was possible to dry the AuNPs assemblies and to solubilize them back with HS-PEGs, improving the colorimetric signal generation. We used this system for protease sensing in biological fluid. Trypsin was chosen as model enzyme and highly positively charged peptides were conjugated to HS-PEG molecules as cleavage substrate. The increase of positive charge of the HS-PEG-peptide conjugate quenched the dissociation capacity of the HS-PEG molecules which could only be restored by the proteolytic cleavage. Picomolar limit of detection was obtained as well as the detection in saliva or urine. TOC O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=111 SRC="FIGDIR/small/508454v1_ufig1.gif" ALT="Figure 1"> View larger version (44K): org.highwire.dtl.DTLVardef@13a6f3org.highwire.dtl.DTLVardef@35b42dorg.highwire.dtl.DTLVardef@1c8249forg.highwire.dtl.DTLVardef@dc8236_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioengineering↗

bioRxiv2022

Microbiota-stimulated Interleukin-22 regulates brain neurons and protects against stress-induced anxiety

Psychological stress and its sequelae are a major public health problem. While the immune system has been implicated in the development of stress-related disorders, how the immune signals modulate neural responses to stress is poorly understood. Contrary to our expectations, we found that the immune cytokine Interleukin (IL)-22 is the key mediator of an immune-to-brain pathway that diminishes, rather than amplifies, stress-induced anxiety. We showed that stress induced TH17 differentiation and IL-22 production in the intestine following barrier dysfunction and microbiota stimulation. IL-22 then directly signaled to septal neurons in the brain to mitigate anxiety-like behavior. Accordingly, mice treated with exogenous IL-22 showed resilience to chronic stress-induced anxiety disorders. Our study thus reveals a previously-unappreciated immune-to-brain axis that defends against psychological stress, suggesting a potential intervention strategy for stress-related mental diseases.

immunology↗

bioRxiv2022

Geometric effects in gas vesicle buckling under ultrasound

Acoustic reporter genes based on gas vesicles (GVs) have enabled the use of ultrasound to noninvasively visualize cellular function in vivo. The specific detection of GV signals relative to background acoustic scattering in tissues is facilitated by nonlinear ultrasound imaging techniques taking advantage of the sonomechanical buckling of GVs. However, the effect of geometry on the buckling behavior of GVs under exposure to ultrasound has not been studied. To understand such geometric effects, we developed computational models of GVs of various lengths and diameters and used finite element simulations to predict their threshold buckling pressures and post-buckling deformations. We demonstrated that the GV diameter has an inverse cubic relation to the threshold buckling pressure, whereas length has no substantial effect. To complement these simulations, we experimentally probed the effect of geometry on the mechanical properties of GVs and the corresponding nonlinear ultrasound signals. The results of these experiments corroborate our computational predictions. This study provides fundamental insights into how geometry affects the sonomechanical properties of GVs, which, in turn, can inform further engineering of these nanostructures for high-contrast, nonlinear ultrasound imaging. STATEMENT OF SIGNIFICANCEGas vesicles (GVs) are an emerging class of genetically encodable and engineerable imaging agents for ultrasound whose sonomechanical buckling generates nonlinear contrast to enable sensitive and specific imaging in highly scattering biological systems. Though the effect of protein composition on GV buckling has been studied, the effect of geometry has not previously been addressed. This study reveals that geometry, especially GV diameter, significantly alters the threshold acoustic pressures required to induce GV buckling. Our computational predictions and experimental results provide fundamental understanding of the relationship between GV geometry and buckling properties and underscore the utility of GVs for nonlinear ultrasound imaging. Additionally, our results provide suggestions to further engineer GVs to enable in vivo ultrasound imaging with greater sensitivity and higher contrast.

biophysics↗

bioRxiv2022

KLF7 Promotes Preadipocyte Proliferation via Activation of the Akt Signaling Pathway by Cis-regulating CDKN3

Kruppel-like transcription factor 7 (KLF7) promotes preadipocyte proliferation; however, its target gene in this process has not yet been identified. Using KLF7 ChIP-seq analysis, we previously showed that a KLF7-binding peak is present upstream of the cyclin-dependent kinase inhibitor 3 gene (CDKN3) in chicken preadipocytes. In the current study, we identified CDKN3 as a target gene of KLF7 that mediates the effects of KLF7 on preadipocyte proliferation. Furthermore, 5'-truncating mutation analysis showed that the minimal promoter was located between CDKN3 nt -160 and nt -7 (relative to the translation initiation codon ATG). KLF7 overexpression increased CDKN3 promoter activity in the DF-1 and immortalized chicken preadipocyte (ICP1) cell lines. Deletion of the putative binding site of KLF7 abolished the promotive effect of KLF7 overexpression on CDKN3 promoter activity. Moreover, CDKN3-knockdown and -overexpression assays revealed that CDKN3 enhanced ICP1 cell proliferation. Flow cytometry analysis showed that CDKN3 accelerated the G1/S transition. Further, we found that KLF7 promoted ICP1 cell proliferation via Akt phosphorylation by regulating CDKN3. Taken together, these results suggest that KLF7 promotes preadipocyte proliferation via activating the Akt signaling pathway by cis-regulating CDKN3, thus driving the G1/S transition.

molecular biology↗

bioRxiv2022

An attempt to find the correlations between body weight and the composition of gut microbiota in Zhejiang and Shanghai

Previous studies showed that the human gut microbiota was associated with metabolic diseases, but the interaction and mechanism between the gut microbiota and metabolic disease are still unclear. In this study, the gut microbiota of 58 persons living in Zhejiang and Shanghai area will be analyzed. Then, the potential contribution of the human gut microbiota to obesity/high Body Mass Index (BMI) will be explored. The gut microbiota was studied by high throughput sequencing analysis of bacterial 16S rRNA gene fragments, and the gut microbiota samples with different BMI were compared. Meanwhile, some gut microorganisms from faeces of a healthy individual were cultivated and isolated, and the classification was identified by 16S rRNA sequencing. The main microbes in human gut microbiota were assigned to the phyla of Firmicutes, Bacteroidetes, Proteobacteria, and Actinobacteria. Moreover, four strains were isolated from an individual fecal sample, of which one species was assigned to Escherichia fergusonii and the other three strains were assigned to Weissella cibaria. These four species belong to both abundant and low-abundant species revealed by high throughput sequencing. It was found that individuals with different BMI have different gut microbiota; while the differences are not significant. Also, the Firmicutes/Bacteroidetes ratio increases with the decrease of BMI, which is corresponding to previous results. In the future, more cohort gut microbiota in Zhejiang and Shanghai area will be collected and recovered, and the gut microbiota database of Zhejiang and Shanghai area will be built up in order to provide the basis for future gut microbiota modulation in this area.

microbiology↗

bioRxiv2022

CRISPR-based targeted haplotype-resolved assemblies of a megabase region

Constructing high-quality haplotype-resolved genome assemblies has substantially improved the ability to detect and characterize genetic variants. A targeted approach providing readily access to the rich information from haplotype-resolved genome assemblies will be appealing to groups of basic researchers and medical scientists focused on specific genomic regions. Here, using the 4.5 megabase, notoriously difficult-to-assemble major histocompatibility complex (MHC) region as an example, we demonstrated an approach to construct haplotype-resolved de novo assemblies of targeted genomic regions with the CRISPR-based enrichment. Compared to the results from haplotype-resolved genome assemblies, our targeted approach achieved comparable completeness and accuracy with greatly reduced computing complexity, sequencing cost, as well as the amount of starting materials. Moreover, using the targeted assembled personal haplotypes as the reference both improves the quantification accuracy for sequencing data and enables allele-specific functional genomics analyses. Given its highly efficient use of resources, our approach can greatly facilitate population genetic studies of targeted regions, and may pave a new way to elucidate the molecular mechanisms in disease etiology.

genomics↗

bioRxiv2021

Temporal-sensitive prefrontal involvement in associating confidence with task performance illustrates metacognitive introspection in Old World monkeys (Macaca mulatta)

Metacognition refers to the ability to be aware of ones own cognition. Ample evidence indicates that metacognition in the human primate is highly dissociable from cognition, specialized across domains, and subserved by distinct neural substrates. However, these aspects remain relatively understudied in macaque monkeys. In the present study, we investigated the functionality of macaque metacognition by combining a confidence proxy, hierarchical Bayesian meta-d' computational modelling, and a single-pulse transcranial magnetic stimulation technique. We found that Brodmann area 46d (BA46d) played a critical role in supporting metacognition independent of task performance; we also found that the critical role of this region in meta-calculation was time-sensitive. Additionally, we report that macaque metacognition is highly domain-specific with respect to memory and perception decisions. These findings carry implications for our understanding of metacognitive introspection within the primate lineage.

neuroscience↗

bioRxiv2021

State-of-the-art EEG artifact removal evaluation

ObjectElectroencephalography (EEG) signals suffer from a low signal-to-noise ratio and are very susceptible to muscular, ambient noise, and other artifacts. Many artifact removal algorithms have been proposed to address this problem. However, the evaluation of these algorithms is conventionally too indirect (e.g., black-box comparisons of brain-computer interface performance before and after removal) because it is unclear which part of the signal represents raw EEG and which is noise. This project objectively benchmarks popular artifact removal algorithms and evaluates the fundamental Independent Component Analysis (ICA) approach thanks to a unique dataset where EEG is recorded simultaneously with other physiological signals-facial electromyography (EMG), accelerometers, and gyroscope-while ten subjects perform several repetitions of common artifact-inflicting tasks (blinking, speaking, etc.). ApproachI have compared the correlation between EEG signals and the artifact-representing channels before and after applying an artifact removal algorithm across the different artifact-inflicting tasks. The extent to which an artifact removal method can reduce this correlation objectively quantifies its effectiveness for the different artifacts. In the same direction, I have determined to what extent ICA successfully detects artefactual components in EEG by comparing the corresponding correlations for independent components that are labelled as artifacts with those labeled as EEG. Main resultThe FORCe was found to be the most effective and generic artifact removal method, cleaning almost 40% of artifacts. ICA is shown to be able to isolate almost 70% of artefactual components. SignificanceThis work alleviates the problem of unreliable evaluation of EEG artifact removal frameworks and provides the first reliable benchmark for the most popular algorithms in this literature.

neuroscience↗

bioRxiv2021

Ultrafast amplitude modulation for molecular and hemodynamic ultrasound imaging

Ultrasound is playing an emerging role in molecular and cellular imaging thanks to new micro- and nanoscale contrast agents and reporter genes. Acoustic methods for the selective in vivo detection of these imaging agents are needed to maximize their impact in biology and medicine. Existing ultrasound pulse sequences use the nonlinearity in contrast agents response to acoustic pressure to distinguish them from mostly linear tissue scattering. However, such pulse sequences typically scan the sample using focused transmissions, resulting in a limited frame rate and restricted field of view. Meanwhile, existing wide-field scanning techniques based on plane wave transmissions suffer from limited sensitivity or nonlinear artifacts. To overcome these limitations, we introduce an ultrafast nonlinear imaging modality combining amplitude-modulated pulses, multiplane wave transmissions and selective coherent compounding. This technique achieves contrast imaging sensitivity comparable to much slower gold-standard amplitude modulation sequences and enables the acquisition of larger and deeper fields of view, while providing a much faster imaging framerate of 3.2kHz. Additionally, it enables simultaneous nonlinear and linear image formation, and allows concurrent monitoring of phenomena accessible only at ultrafast framerates, such as blood volume variations. We demonstrate the performance of this ultrafast amplitude modulation (uAM) technique by imaging gas vesicles, an emerging class of genetically encodable biomolecular contrast agents, in several in vitro and in vivo contexts. These demonstrations include the rapid discrimination of moving contrast agents and the real-time monitoring of phagolysosomal function in the mouse liver.

bioengineering↗

bioRxiv2021

Genomically Mined Acoustic Reporter Genes Enable On-Demand In Vivo Monitoring of Tumor-Homing Bacteria

A major outstanding challenge in the fields of biological research, synthetic biology and cell-based medicine is visualizing the function of natural and engineered cells noninvasively inside opaque organisms. Ultrasound imaging has the potential to address this challenge as a widely available technique with a tissue penetration of several centimeters and spatial resolution below 100 m. Recently, the first genetically encoded acoustic reporters were developed based on bacterial gas vesicles to link ultrasound signals to molecular and cellular function. However, the properties of these first-generation acoustic reporter genes (ARGs) resulted in limited sensitivity and specificity for imaging gene expression in vivo. Here, we describe second-generation ARGs with greatly improved acoustic properties and expression characteristics, identified through a phylogenetic screen of candidate gene clusters from diverse bacteria and archaea. The resulting constructs offer major qualitative and quantitative improvements, including much stronger ultrasound contrast, the ability to produce nonlinear signals distinguishable from background tissue, and stable long-term expression. We demonstrate the capabilities of these next-generation ARGs by imaging in situ gene expression in mouse models of breast cancer and tumor-homing therapeutic bacteria, noninvasively revealing the unique spatial distributions of tumor growth and colonization by therapeutic cells in living subjects and providing real-time guidance for interventions such as needle biopsies.

bioengineering↗