Spatial genomics enables multi-modal study of clonal heterogeneity in tissues.

The state and behaviour of a cell can be influenced by both genetic and environmental factors. In particular, tumour progression is determined by underlying genetic aberrations1-4 as well as the makeup of the tumour microenvironment5,6. Quantifying the contributions of these factors requires new technologies that can accurately measure the spatial location of genomic sequence together with phenotypic readouts. Here we developed slide-DNA-seq, a method for capturing spatially resolved DNA sequences from intact tissue sections. We demonstrate that this method accurately preserves local tumour architecture and enables the de novo discovery of distinct tumour clones and their copy number alterations. We then apply slide-DNA-seq to a mouse model of metastasis and a primary human cancer, revealing that clonal populations are confined to distinct spatial regions. Moreover, through integration with spatial transcriptomics, we uncover distinct sets of genes that are associated with clone-specific genetic aberrations, the local tumour microenvironment, or both. Together, this multi-modal spatial genomics approach provides a versatile platform for quantifying how cell-intrinsic and cell-extrinsic factors contribute to gene expression, protein abundance and other cellular phenotypes.

Genetic architecture of ecological divergence between Oryza rufipogon and Oryza nivara.

Ecological divergence due to habitat difference plays a prominent role in the formation of new species, but the genetic architecture during ecological speciation and the mechanism underlying phenotypic divergence remain less understood. Two wild ancestors of rice (Oryza rufipogon and Oryza nivara) are a progenitor-derivative species pair with ecological divergence and provide a unique system for studying ecological adaptation/speciation. Here, we constructed a high-resolution linkage map and conducted a quantitative trait locus (QTL) analysis of 19 phenotypic traits using an F2 population generated from a cross between the two Oryza species. We identified 113 QTLs associated with interspecific divergence of 16 quantitative traits, with effect sizes ranging from 1.61% to 34.1% in terms of the percentage of variation explained (PVE). The distribution of effect sizes of QTLs followed a negative exponential, suggesting that a few genes of large effect and many genes of small effect were responsible for the phenotypic divergence. We observed 18 clusters of QTLs (QTL hotspots) on 11 chromosomes, significantly more than that expected by chance, demonstrating the importance of coinheritance of loci/genes in ecological adaptation/speciation. Analysis of effect direction and v-test statistics revealed that interspecific differentiation of most traits was driven by divergent natural selection, supporting the argument that ecological adaptation/speciation would proceed rapidly under coordinated selection on multiple traits. Our findings provide new insights into the understanding of genetic architecture of ecological adaptation and speciation in plants and help effective manipulation of specific genes or gene cluster in rice breeding.

Pairwise Tomlinson-Harashima precoding for multiple-lane IM-DD transmissions.

As for the photonic interconnection based on the multiple-lane intensity modulation direct detection (IM-DD) transmission, both intra-channel inter-symbol-interference (ISI) originating from bandwidth constraint, and inter-channel performance discrepancy emerging from inter-channel component differences are the major bottleneck for the throughput enhancement. Here, we propose a pairwise Tomlinson-Harshima precoding (P-THP) scheme, in order to simultaneously deal with both intra-channel ISI and inter-channel performance discrepancy. The effective function of the proposed P-THP scheme is experimentally evaluated by transmitting 4-channel 81-GBaud PAM4 signals over 2 km standard single-mode fiber (SSMF). Compared with the conventional scheme with only applying THP on individual wavelength channel, the required optical received power (ROP) under the back-to-back (B2B) transmission can be reduced by 0.75∼1 dB with the help of proposed P-THP in different experimental component configurations, at the 7% hard decision forward error correction (HD-FEC) threshold of BER = 3.8 × 10-3. After the 2 km SSMF transmission, only the use of proposed P-THP can guarantee to reach the designated HD-FEC threshold, leading to a net rate of >600 Gbit/s.

Bias-drift insensitive full-field frequency response characterization of a thin-film lithium niobate-based intensity modulator.

We propose a rapid and precise scheme for characterizing the full-field frequency response of a thin-film lithium niobate-based intensity modulator (TFLN-IM) via a specially designed multi-tone microwave signal. Our proposed scheme remains insensitive to the bias-drift of IM. Experimental verification is implemented with a self-packaged TFLN-IM with a 3 dB bandwidth of 30 GHz. In comparison with the vector network analyzer (VNA) characterization results, the deviation values of the amplitude-frequency response (AFR) and phase-frequency response (PFR) within the 50 GHz bandwidth are below 0.3 dB and 0.15 rad, respectively. When the bias is drifted within 90% of the Vπ range, the deviation fluctuation values of AFR and PFR are less than 0.3 dB and 0.05 rad, respectively. With the help of the full-field response results, we can pre-compensate the TFLN-IM for the 64 Gbaud PAM-4 signals under the back-to-back (B2B) transmission, achieving a received optical power (ROP) gain of 2.3 dB. The versatility of our proposed full-field response characterization scheme can extend to various optical transceivers, offering the advantage of low cost, robust operation, and flexible implementation.

On the multipath interference mitigation for high-speed IM-DD transmissions with Nyquist subcarrier modulation.

The performance of high-speed intensity modulation direct detection (IM-DD) transmissions is severely degraded due to the occurrence of multipath interference (MPI), especially when a higher-order modulation format is utilized. Here, we propose and demonstrate, for the first time to the best of our knowledge, that a Nyquist subcarrier modulation (Nyquist-SCM) format inherently exhibits resistance to the MPI. We experimentally evaluate the MPI tolerance by transmitting 56 Gbit/s PAM-4 signals and Nyquist-SCM 16QAM signals over the 2 km standard single-mode fiber (SSMF) when the C-band semiconductor laser with a linewidth of 1.7 MHz is utilized. In comparison with the PAM-4 format, the Nyquist-SCM 16QAM format can lead to an enhanced MPI tolerance of 4 dB at the KP4-FEC threshold of BER = 2 × 10-4. In addition, even with the help of MPI mitigation for the PAM-4 signals based on two newly reported methods, the utilization of Nyquist-SCM 16QAM signal can still guarantee an improved MPI tolerance of 1 dB.

Evolution-Based Discovery of Polyketide Acylated Valine from a Cytochalasin-Like Gene Cluster in Simplicillium lamelliciola HDN13430.

Utilizing a gene evolution-oriented approach for gene cluster mining, a cryptic cytochalasin-like gene cluster (sla) in Antarctic-derived Simplicillium lamelliciola HDN13430 was identified. Compared with the canonical cytochalasin biosynthetic gene clusters (BGCs), the sla gene cluster lacks the key α,ß-hydrolase gene. Heterologous expression of the sla gene cluster led to the discovery of a new compound, slamysin (1), characterized by an N-acylated amino acid structure and demonstrating weak anti-Bacillus cereus activity. These findings underscore the potential of genetic evolution in uncovering novel compounds and indicating specific adaptive evolution within specialized habitats.

Characterization of differential modal group delay in few-mode fiber using a digital re-sampling technique.

We characterize the differential modal group delay (DMGD) arising in few-mode fibers (FMFs) based on the digital re-sampling technique, which is commonly used in current digital signal processing flow at the receiver-side. When the DMGD of a 291-m two-mode fiber is characterized over the C-band by using a 500-Mb/s non-return-to-zero (NRZ) signal and 1-GSa/s real-time oscilloscope, the experimental results are consistent with the DMGD obtained from the traditional time-of-flight (TOF) method. However, the wide-bandwidth instruments of the traditional TOF method can be replaced by cheap ones with a bandwidth of only a few hundred MHz, but the same temporal precision is achieved. Moreover, our proposed DMGD characterization method is not limited by the number of guided modes arising in the FMF, together with the capability to obtain both the DMGD value and its sign between two arbitrary guided modes.

Broadband linear frequency modulation signal compression based on a spectral Talbot effect.

Broadband linear frequency modulation (LFM) signals with a long duration are widely used in radar and broadband communication systems. The LFM signals are compressed to a Fourier-transform-limited pulse train after matched filtering, which effectively improves the signal-to-noise ratio (SNR) of detection. Quadratic phase response is the key component of matched filtering, which can be achieved by phase filters or dispersion elements. Suffering from the limited resolution of phase filters and complex equivalent large dispersion structures, pulse compression of broadband LFM signals with a long duration remains an open challenge. In this paper, LFM signal compression based on the spectral Talbot effect is proposed and experimentally demonstrated, where ultra-large equivalent dispersion (around 1.7 × 109 ps/nm) is realized by a simple optical filter ring. Experimentally, the LFM signal with a bandwidth of 12 GHz and a duration of 163 µs is compressed into a Fourier-transform-limited pulse train, which improves the SNR by 24 dB. Moreover, the proposed method also measures the delay difference between two LFM signals, ranging from 0 to 110 ns.

Low latency microwave photonic RTFT processing based on bandwidth slicing and equivalent dispersion.

Microwave photonic real-time Fourier transformation (RTFT) processing based on optical dispersion is a promising solution for microwave spectrum analysis. However, it usually brings the drawbacks of limited frequency resolution and large processing latency. Here, we demonstrate a low-latency microwave photonic RTFT processing based on bandwidth slicing and equivalent dispersion. The input RF signal is first divided into different channels with the help of bandwidth slicing technique, and then finely analyzed by the fiber-loop based frequency-to-time mapping. In the proof-of-concept experiment, a 0.44-m fiber-loop offers an equivalent dispersion as high as 6 × 105 ps/nm with a small transmission latency of 50 ns. As a result, we can realize a wide instantaneous bandwidth of 1.35 GHz, a high frequency resolution of approximately 20 MHz, and a high acquisition frame rate of approximately 450 MHz, together with a total latency of less than 200 ns.

Exfoliation of a Two-Dimensional Metal-Organic Framework for Enhanced Photocatalytic CO2 Reduction.

A two-dimensional metal-organic framework, FICN-12, was constructed from tris[4-(1H-pyrazole-4-yl)phenyl]amine (H3TPPA) ligands and Ni2 secondary building units. The triphenylamine moiety in the H3TPPA ligand readily absorbs UV-visible photons and sensitizes the Ni center to drive photocatalytic CO2 reduction. FICN-12 can be exfoliated into monolayer and few-layer nanosheets with a "top-down" approach, which exposes more catalytic sites and increases its catalytic activity. As a result, the nanosheets (FICN-12-MONs) showed photocatalytic CO and CH4 production rates of 121.15 and 12.17 µmol/g/h, respectively, nearly 1.4 times higher than those of bulk FICN-12.

Optically magnified dispersion of microwave signals with a wide and flexible tunable range.

Tunable microwave dispersion is highly desired for a wide field of microwave signal processing. However, a conventional microwave dispersive delay line usually suffers from either a small dispersion value or a narrow operation bandwidth. Here, we experimentally demonstrate the optically magnified dispersion of a microwave signal with a wide and flexible tunable range, based on a bandwidth-scaling microwave photonic system. The obtained microwave dispersion can therefore be magnified from the corresponding optical dispersion with a magnification factor that can be continuously tuned from 10,000 to 85,000. Meanwhile, a proof-of-concept experiment that includes both compression and stretching of chirped microwave pulses is reported. Microwave dispersion from 1.34 ns/GHz to 10.92 ns/GHz can be secured by the corresponding magnification of an optical dispersion value of 16 ps/nm.

Stepwise selection of natural variations at CTB2 and CTB4a improves cold adaptation during domestication of japonica rice.

The improvement of cold adaptation has contributed to the increased growing area of rice. Standing variation and de novo mutation are distinct natural sources of beneficial alleles in plant adaptation. However, the genetic mechanisms and evolutionary patterns underlying these sources in a single population during crop domestication remain elusive. Here we cloned the CTB2 gene, encoding a UDP-glucose sterol glucosyltransferase, for cold tolerance in rice at the booting stage. A single standing variation (I408V) in the conserved UDPGT domain of CTB2 originated from Chinese Oryza rufipogon and contributed to the cold adaptation of Oryza sativa ssp. japonica. CTB2 is located in a 56.8 kb region, including the previously reported gene CTB4a in which de novo mutation arose c. 3200 yr BP in Yunnan province, China, conferring cold tolerance. Standing variation of CTB2 and de novo mutation of CTB4a underwent stepwise selection to facilitate cold adaptation to expand rice cultivation from high-altitude to high-latitude regions. These results provide an example of stepwise selection on two kinds of variation and describe a new molecular mechanism of cold adaptation in japonica rice.

Differentiation, evolution and utilization of natural alleles for cold adaptability at the reproductive stage in rice.

Genetic studies on cold tolerance at the reproductive stage in rice could lead to significant reductions in yield losses. However, knowledge about the genetic basis and adaptive differentiation, as well as the evolution and utilization of the underlying natural alleles, remains limited. Here, 580 rice accessions in two association panels were used to perform genome-wide association study, and 156 loci associated with cold tolerance at the reproductive stage were identified. Os01g0923600 and Os01g0923800 were identified as promising candidate genes in qCTB1t, a major associated locus. Through population genetic analyses, 22 and 29 divergent regions controlling cold adaptive differentiation inter-subspecies (Xian/Indica and Geng/Japonica) and intra-Geng, respectively, were identified. Joint analyses of four cloned cold-tolerance genes showed that they had different origins and utilizations under various climatic conditions. bZIP73 and OsAPX1 differentiating inter-subspecies evolved directly from wild rice, whereas the novel mutations CTB4a and Ctb1 arose in Geng during adaptation to colder climates. The cold-tolerant Geng accessions have undergone stronger selection under colder climate conditions than other accessions during the domestication and breeding processes. Additive effects of dominant allelic variants of four identified genes have been important in adaptation to cold in modern rice varieties. Therefore, this study provides valuable information for further gene discovery and pyramiding breeding to improve cold tolerance at the reproductive stage in rice.

Topical Lyophilized Targeted Lipid Nanoparticles in the Restoration of Skin Barrier Function following Burn Wound.

Lyophilized keratinocyte-targeted nanocarriers (TLNκ) loaded with locked nucleic acid (LNA) modified anti-miR were developed for topical application to full thickness burn injury. TLNκ were designed to selectively deliver LNA-anti-miR-107 to keratinocytes using the peptide sequence ASKAIQVFLLAG. TLNκ employed DOTAP/DODAP combination pH-responsive lipid components to improve endosomal escape. To minimize interference of clearance by non-targeted cells, especially immune cells in the acute wound microenvironment, surface charge was neutralized. Lyophilization was performed to extend the shelf life of the lipid nanoparticles (LNPs). Encapsulation efficiency of anti-miR in lyophilized TLNκ was estimated to be 96.54%. Cargo stability of lyophilized TLNκ was tested. After 9 days of loading with anti-miR-210, TLNκ was effective in lowering abundance of the hypoxamiR miR-210 in keratinocytes challenged with hypoxia. Keratinocyte uptake of DiD-labeled TLNκ was selective and exceeded 90% within 4 hr. Topical application of hydrogel-dispersed lyophilized TLNκ encapsulating LNA anti-miR-107 twice a week significantly accelerated wound closure and restoration of skin barrier function. TLNκ/anti-miR-107 application depleted miR-107 and upregulated dicer expression, which accelerated differentiation of keratinocytes. Expression of junctional proteins such as claudin-1, loricrin, filaggrin, ZO-1, and ZO-2 were significantly upregulated following TLNκ/anti-miR-107 treatment. These LNPs are promising as topical therapeutic agents in the management of burn injury.

Gnp4/LAX2, a RAWUL protein, interferes with the OsIAA3-OsARF25 interaction to regulate grain length via the auxin signaling pathway in rice.

Grain length is one of the determinants of yield in rice and auxin plays an important role in regulating it by mediating cell growth. Although several genes in the auxin pathway are involved in regulating grain length, the underlying molecular mechanisms remain unclear. In this study we identify a RING-finger and wd40-associated ubiquitin-like (RAWUL) domain-containing protein, Gnp4/LAX2, with a hitherto unknown role in regulation of grain length by its influence on cell expansion. Gnp4/LAX2 is broadly expressed in the plant and subcellular localization analysis shows that it encodes a nuclear protein. Overexpression of Gnp4/LAX2 can significantly increase grain length and thousand-kernel weight. Moreover, Gnp4/LAX2 physically interacts with OsIAA3 and consequently interferes with the OsIAA3-OsARF25 interaction in vitro and in vivo. OsIAA3 RNAi plants consistently exhibit longer grains, while the mutant osarf25 has small grains. In addition, OsARF25 binds to the promoter of OsERF142/SMOS1, a regulator of organ size, and positively regulates its expression. Taken together, the results reveal that Gnp4/LAX2 functions as a regulator of grain length through participation in the OsIAA3-OsARF25-OsERF142 pathway and that it has potential value for molecular breeding in rice.

Real-time Fourier transformation based on the bandwidth magnification of RF signals.

We demonstrate a novel real-time Fourier transformation scheme with megahertz-level resolution realized by bandwidth magnification of radio frequency (RF) signals. Before the frequency-to-time mapping, the RF signal is modulated on an optical frequency comb, and then extracted by a Vernier comb filter. As a result, RF components can be separated in the spectrum with a greatly magnified optical bandwidth. Thus, even with limited dispersion provided by an ordinary optical fiber, the frequency-dependent pulses can be distinguished in the time domain. Experimentally, the RF signal with the frequency difference of 60 MHz is separated by around 123 ps in the time domain, equivalent to the dispersion of 1975.5 ps/GHz (2.47×105 ps/nm), while the physical dispersion is 1500 ps/nm. Thus, based on the bandwidth magnification of signals, the dispersion is equivalently amplified by 165 times.

Megahertz-resolution programmable microwave shaper.

A novel microwave shaper is proposed and demonstrated, of which the microwave spectral transfer function could be fully programmable with high resolution. We achieve this by bandwidth-compressed mapping a programmable optical wave-shaper, which has a lower frequency resolution of tens of gigahertz, to a microwave one with resolution of tens of megahertz. This is based on a novel technology of "bandwidth scaling," which employs bandwidth-stretched electronic-to-optical conversion and bandwidth-compressed optical-to-electronic conversion. We demonstrate the high resolution and full reconfigurability experimentally. Furthermore, we show the group delay variation could be greatly enlarged after mapping; this is then verified by the experiment with an enlargement of 194 times. The resolution improvement and group delay magnification significantly distinguish our proposal from previous optics-to-microwave spectrum mapping.

Fine mapping of QTL qCTB10-2 that confers cold tolerance at the booting stage in rice.

KEY MESSAGE: The QTL qCTB10 - 2 controlling cold tolerance at the booting stage in rice was delimited to a 132.5 kb region containing 17 candidate genes and 4 genes were cold-inducible. Low temperature at the booting stage is a major abiotic stress-limiting rice production. Although some QTL for cold tolerance in rice have been reported, fine mapping of those QTL effective at the booting stage is few. Here, the near-isogenic line ZL31-2, selected from a BC7F2 population derived from a cross between cold-tolerant variety Kunmingxiaobaigu (KMXBG) and the cold-sensitive variety Towada, was used to map a QTL on chromosome 10 for cold tolerance at the booting stage. Using BC7F3 and BC7F4 populations, we firstly confirmed qCTB10-2 and gained confidence that it could be fine mapped. QTL qCTB10-2 explained 13.9 and 15.9% of the phenotypic variances in those two generations, respectively. Using homozygous recombinants screened from larger BC7F4 and BC7F5 populations, qCTB10-2 was delimited to a 132.5 kb region between markers RM25121 and MM0568. 17 putative predicted genes were located in the region and only 5 were predicted to encode expressed proteins. Expression patterns of these five genes demonstrated that, except for constant expression of LOC_Os10g11820, LOC_Os10g11730, LOC_Os10g11770, and LOC_Os10g11810 were highly induced by cold stress in ZL31-2 compared to Towada, while LOC_Os10g11750 showed little difference. Our results provide a basis for identifying the genes underlying qCTB10-2 and indicate that markers linked to the qCTB10-2 locus can be used to improve the cold tolerance of rice at the booting stage by marker-assisted selection.

FRAGSION: ultra-fast protein fragment library generation by IOHMM sampling.

MOTIVATION: Speed, accuracy and robustness of building protein fragment library have important implications in de novo protein structure prediction since fragment-based methods are one of the most successful approaches in template-free modeling (FM). Majority of the existing fragment detection methods rely on database-driven search strategies to identify candidate fragments, which are inherently time-consuming and often hinder the possibility to locate longer fragments due to the limited sizes of databases. Also, it is difficult to alleviate the effect of noisy sequence-based predicted features such as secondary structures on the quality of fragment. RESULTS: Here, we present FRAGSION, a database-free method to efficiently generate protein fragment library by sampling from an Input-Output Hidden Markov Model. FRAGSION offers some unique features compared to existing approaches in that it (i) is lightning-fast, consuming only few seconds of CPU time to generate fragment library for a protein of typical length (300 residues); (ii) can generate dynamic-size fragments of any length (even for the whole protein sequence) and (iii) offers ways to handle noise in predicted secondary structure during fragment sampling. On a FM dataset from the most recent Critical Assessment of Structure Prediction, we demonstrate that FGRAGSION provides advantages over the state-of-the-art fragment picking protocol of ROSETTA suite by speeding up computation by several orders of magnitude while achieving comparable performance in fragment quality. AVAILABILITY AND IMPLEMENTATION: Source code and executable versions of FRAGSION for Linux and MacOS is freely available to non-commercial users at http://sysbio.rnet.missouri.edu/FRAGSION/ It is bundled with a manual and example data. CONTACT: chengji@missouri.edu SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Real-time frequency-to-time mapping based on spectrally-discrete chromatic dispersion.

Traditional photonics-assisted real-time Fourier transform (RTFT) usually suffers from limited chromatic dispersion, huge volume, or large time delay and attendant loss. In this paper we propose frequency-to-time mapping (FTM) by spectrally-discrete dispersion to increase frequency sensitivity greatly. The novel media has periodic ON/OFF intensity frequency response while quadratic phase distribution along disconnected channels, which de-chirps matched optical input to repeated Fourier-transform-limited output. Real-time FTM is then obtained within each period. Since only discrete phase retardation rather than continuously-changed true time delay is required, huge equivalent dispersion is then available by compact device. Such FTM is theoretically analyzed, and implementation by cascaded optical ring resonators is proposed. After a numerical example, our theory is demonstrated by a proof-of-concept experiment, where a single loop containing 0.5-meters-long fiber is used. FTM under 400-MHz unambiguous bandwidth and 25-MHz resolution is reported. Highly-sensitive and linear mapping is achieved with 6.25 ps/MHz, equivalent to ~4.6 × 104-km standard single mode fiber. Extended instantaneous bandwidth is expected by ring cascading. Our proposal may provide a promising method for real-time, low-latency Fourier transform.