Canopy occupation volume as an indicator of canopy photosynthetic capacity.

Leaf angle and leaf area index together influence canopy light interception and canopy photosynthesis. However, so far, there is no effective method to identify the optimal combination of these two parameters for canopy photosynthesis. In this study, first a robust high-throughput method for accurate segmentation of maize organs based on 3D point clouds data was developed, then the segmented plant organs were used to generate new 3D point clouds for the canopy of altered architectures. With this, we simulated the synergistic effect of leaf area and leaf angle on canopy photosynthesis. The results show that, compared to the traditional parameters describing the canopy photosynthesis including leaf area index, facet angle and canopy coverage, a new parameter - the canopy occupation volume (COV) - can better explain the variations of canopy photosynthetic capacity. Specifically, COV can explain > 79% variations of canopy photosynthesis generated by changing leaf angle and > 84% variations of canopy photosynthesis generated by changing leaf area. As COV can be calculated in a high-throughput manner based on the canopy point clouds, it can be used to evaluate canopy architecture in breeding and agronomic research.

Overexpression of maize transcription factor mEmBP-1 increases photosynthesis, biomass, and yield in rice.

Identifying new options to improve photosynthetic capacity is a major approach to improve crop yield potential. Here we report that overexpression of the gene encoding the transcription factor mEmBP-1 led to simultaneously increased expression of many genes in photosynthesis, including genes encoding Chl a,b-binding proteins (Lhca and Lhcb), PSII (PsbR3 and PsbW) and PSI reaction center subunits (PsaK and PsaN), chloroplast ATP synthase subunit, electron transport reaction components (Fd1 and PC), and also major genes in the Calvin-Benson-Bassham cycle, including those encoding Rubisco, glyceraldehyde phosphate dehydrogenase, fructose bisphosphate aldolase, transketolase, and phosphoribulokinase. These increased expression of photosynthesis genes resulted in increased leaf chlorophyll pigment, photosynthetic rate, biomass growth, and grain yield both in the greenhouse and in the field. Using EMSA experiments, we showed that mEmBP-1a protein can directly bind to the promoter region of photosynthesis genes, suggesting that the direct binding of mEmBP-1a to the G-box domain of photosynthetic genes up-regulates expression of these genes. Altogether, our results show that mEmBP-1a is a major regulator of photosynthesis, which can be used to increase rice photosynthesis and yield in the field.

Decomposition analysis on soybean productivity increase under elevated CO2 using 3-D canopy model reveals synergestic effects of CO2 and light in photosynthesis.

BACKGROUND AND AIMS: Understanding how climate change influences crop productivity helps in identifying new options to increase crop productivity. Soybean is the most important dicotyledonous seed crop in terms of planting area. Although the impacts of elevated atmospheric [CO2] on soybean physiology, growth and biomass accumulation have been studied extensively, the contribution of different factors to changes in season-long whole crop photosynthetic CO2 uptake [gross primary productivity (GPP)] under elevated [CO2] have not been fully quantified. METHODS: A 3-D canopy model combining canopy 3-D architecture, ray tracing and leaf photosynthesis was built to: (1) study the impacts of elevated [CO2] on soybean GPP across a whole growing season; (2) dissect the contribution of different factors to changes in GPP; and (3) determine the extent, if any, of synergism between [CO2] and light on changes in GPP. The model was parameterized from measurements of leaf physiology and canopy architectural parameters at the soybean Free Air CO2 Enrichment (SoyFACE) facility in Champaign, Illinois. KEY RESULTS: Using this model, we showed that both a CO2 fertilization effect and changes in canopy architecture contributed to the large increase in GPP while acclimation in photosynthetic physiological parameters to elevated [CO2] and altered leaf temperature played only a minor role in the changes in GPP. Furthermore, at early developmental stages, elevated [CO2] increased leaf area index which led to increased canopy light absorption and canopy photosynthesis. At later developmental stages, on days with high ambient light levels, the proportion of leaves in a canopy limited by Rubisco carboxylation increased from 12.2 % to 35.6 %, which led to a greater enhancement of elevated [CO2] to GPP. CONCLUSIONS: This study develops a new method to dissect the contribution of different factors to responses of crops under climate change. We showed that there is a synergestic effect of CO2 and light on crop growth under elevated CO2 conditions.

Long-Term Outcomes of Transarterial Chemoembolization Combined with Radiofrequency Ablation Versus Transarterial Chemoembolization Alone for Recurrent Hepatocellular Carcinoma After Surgical Resection.

BACKGROUND: There is lack of data for identifying optimal local therapy for the management of recurrent hepatocellular carcinoma (HCC) after hepatic resection. AIMS: A retrospective study was performed to compare the effectiveness of transarterial chemoembolization (TACE) plus radiofrequency ablation (RFA) with that of TACE alone for recurrent HCC. METHODS: From 2007 to 2013, patients with recurrent HCC ≤ 5 cm were treated with either TACE plus RFA (n = 96) or TACE (n = 63). Inverse probability of treatment weighting was used to make allowances for imbalances in treatment assignment. The disease-free survival (DFS) and overall survival (OS) were retrospectively analyzed. RESULTS: The TACE group had lower pretreatment Child-Pugh class (P = 0.025) and shorter pretreatment interval of recurrence (P = 0.028). The 1-, 3-, and 5-year DFS rates for the TACE-RFA group were 55.1%, 22.5%, and 9.7%, respectively, and 41.1%, 9.9%, and 4.9%, respectively, for the TACE group. The OS rates at 1, 3, and 5 years were 82.3%, 42.7%, and 16.5%, respectively, in the TACE-RFA group, and 75.9%, 30.7%, and 11.3%, respectively, in the TACE group. Cirrhosis was significantly associated with disease progression (hazard ratio [HR] 1.53; 95% CI 1.09-2.14; P = 0.014). CONCLUSIONS: In patients with recurrent HCC ≤ 5 cm, TACE-RFA shows better DFS than TACE alone as a first-line local therapy.

Germline Duplication of SNORA18L5 Increases Risk for HBV-related Hepatocellular Carcinoma by Altering Localization of Ribosomal Proteins and Decreasing Levels of p53.

BACKGROUND & AIMS: Single nucleotide polymorphisms could affect risk for hepatitis B virus (HBV)-related hepatocellular carcinoma (HCC). We performed a germline copy number variation (CNV)-based genome-wide association study (GWAS) in populations of Chinese ancestry to search for germline CNVs that increase risk of HCC. METHODS: We conducted a CNV-based GWAS of 1583 HCC cases (persons with chronic HBV infection and HCC) and 1540 controls (persons with chronic HBV infection without HCC) in Chinese populations. Identified candidates were expressed in L-02, HepG2, or TP53-/- or wild-type HCT116 cells, and knocked down with short hairpin RNAs in HepG2, Bel-7402, and SMMC-7721 cells; proliferation, colony formation, and apoptosis were measured. Formation of xenograft tumors from cell lines was monitored in nude mice. Subcellular localization of ribosome proteins and levels or activity of p53 were investigated by co-immunoprecipitation, immunofluorescence, and immunoblot analyses. Levels of small nucleolar RNA H/ACA box 18-like 5 (SNORA18L5) were quantified by quantitative reverse transcription polymerase chain reaction. RESULTS: We identified a low-frequency duplication at chromosome 15q13.3 strongly associated with risk of HBV-related HCC (overall P = 3.17 × 10-8; odds ratio, 12.02). Copy numbers of the 15q13.3 duplication correlated with the expression of SNORA18L5 in liver tissues. Overexpression of SNORA18L5 increased HCC cell proliferation and growth of xenograft tumors in mice; knockdown reduced HCC proliferation and tumor growth. SNORA18L5 overexpression in HepG2 and SMMC-7721 cells inhibited p53-dependent cell cycle arrest and apoptosis. Overexpression of SNORA18L5 led to hyperactive ribosome biogenesis, increasing levels of mature 18S and 28S ribosomal RNAs and causing the ribosomal proteins RPL5 and RPL11 to stay in the nucleolus, which kept them from binding to MDM2. This resulted in increased MDM2-mediated ubiquitination and degradation of p53. Levels of SNORA18L5 were increased in HCC tissues compared with nontumor liver tissues and associated with shorter survival times of patients. CONCLUSIONS: In a CNV-based GWAS, we associated duplication at 15q13.3 with increased risk of HBV-related HCC. We found SNORA18L5 at this location to promote HCC cell proliferation and tumor growth in mice. SNORA18L5 increases ribosome biogenesis, facilitates ribosomal RNA maturation, and alters localization of RPL5 and RPL11, allowing for increased MDM2-mediated proteolysis of p53 and cell cycle arrest.

A three-dimensional canopy photosynthesis model in rice with a complete description of the canopy architecture, leaf physiology, and mechanical properties.

In current rice breeding programs, morphological parameters such as plant height, leaf length and width, leaf angle, panicle architecture, and tiller number during the grain filling stage are used as major selection targets. However, so far, there is no robust approach to quantitatively define the optimal combinations of parameters that can lead to increased canopy radiation use efficiency (RUE). Here we report the development of a three-dimensional canopy photosynthesis model (3dCAP), which effectively combines three-dimensional canopy architecture, canopy vertical nitrogen distribution, a ray-tracing algorithm, and a leaf photosynthesis model. Concurrently, we developed an efficient workflow for the parameterization of 3dCAP. 3dCAP predicted daily canopy RUE for different nitrogen treatments of a given rice cultivar under different weather conditions. Using 3dCAP, we explored the influence of three canopy architectural parameters-tiller number, tiller angle and leaf angle-on canopy RUE. Under different weather conditions and different nitrogen treatments, canopy architecture optimized by manipulating these parameters can increase daily net canopy photosynthetic CO2 uptake by 10-52%. Generally, a smaller tiller angle was predicted for most elite rice canopy architectures, especially under scattered light conditions. Results further show that similar canopy RUE can be obtained by multiple different parameter combinations; these combinations share two common features of high light absorption by leaves in the canopy and a high level of coordination between the nitrogen concentration and the light absorbed by each leaf within the canopy. Overall, this new model has potential to be used in rice ideotype design for improved canopy RUE.

Leaf Photosynthetic Parameters Related to Biomass Accumulation in a Global Rice Diversity Survey.

Mining natural variations is a major approach to identify new options to improve crop light use efficiency. So far, successes in identifying photosynthetic parameters positively related to crop biomass accumulation through this approach are scarce, possibly due to the earlier emphasis on properties related to leaf instead of canopy photosynthetic efficiency. This study aims to uncover rice (Oryza sativa) natural variations to identify leaf physiological parameters that are highly correlated with biomass accumulation, a surrogate of canopy photosynthesis. To do this, we systematically investigated 14 photosynthetic parameters and four morphological traits in a rice population, which consists of 204 U.S. Department of Agriculture-curated minicore accessions collected globally and 11 elite Chinese rice cultivars in both Beijing and Shanghai. To identify key components responsible for the variance of biomass accumulation, we applied a stepwise feature-selection approach based on linear regression models. Although there are large variations in photosynthetic parameters measured in different environments, we observed that photosynthetic rate under low light (Alow) was highly related to biomass accumulation and also exhibited high genomic inheritability in both environments, suggesting its great potential to be used as a target for future rice breeding programs. Large variations in Alow among modern rice cultivars further suggest the great potential of using this parameter in contemporary rice breeding for the improvement of biomass and, hence, yield potential.

Systems model-guided rice yield improvements based on genes controlling source, sink, and flow.

A large number of genes related to source, sink, and flow have been identified after decades of research in plant genetics. Unfortunately, these genes have not been effectively utilized in modern crop breeding. This perspective paper aims to examine the reasons behind such a phenomenon and propose a strategy to resolve this situation. Specifically, we first systematically survey the currently cloned genes related to source, sink, and flow; then we discuss three factors hindering effective application of these identified genes, which include the lack of effective methods to identify limiting or critical steps in a signaling network, the misplacement of emphasis on properties, at the leaf, instead of the whole canopy level, and the non-linear complex interaction between source, sink, and flow. Finally, we propose the development of systems models of source, sink and flow, together with a detailed simulation of interactions between them and their surrounding environments, to guide effective use of the identified elements in modern rice breeding. These systems models will contribute directly to the definition of crop ideotype and also identification of critical features and parameters that limit the yield potential in current cultivars.

A user-friendly means to scale from the biochemistry of photosynthesis to whole crop canopies and production in time and space - development of Java WIMOVAC.

Windows Intuitive Model of Vegetation response to Atmosphere and Climate Change (WIMOVAC) has been used widely as a generic modular mechanistically rich model of plant production. It can predict the responses of leaf and canopy carbon balance, as well as production in different environmental conditions, in particular those relevant to global change. Here, we introduce an open source Java user-friendly version of WIMOVAC. This software is platform independent and can be easily downloaded to a laptop and used without any prior programming skills. In this article, we describe the structure, equations and user guide and illustrate some potential applications of WIMOVAC.

The impact of modifying photosystem antenna size on canopy photosynthetic efficiency-Development of a new canopy photosynthesis model scaling from metabolism to canopy level processes.

Canopy photosynthesis (Ac ) describes photosynthesis of an entire crop field and the daily and seasonal integrals of Ac positively correlate with daily and seasonal biomass production. Much effort in crop breeding has focused on improving canopy architecture and hence light distribution inside the canopy. Here, we develop a new integrated canopy photosynthesis model including canopy architecture, a ray tracing algorithm, and C3 photosynthetic metabolism to explore the option of manipulating leaf chlorophyll concentration ([Chl]) for greater Ac and nitrogen use efficiency (NUE). Model simulation results show that (a) efficiency of photosystem II increased when [Chl] was decreased by decreasing antenna size and (b) the light received by leaves at the bottom layers increased when [Chl] throughout the canopy was decreased. Furthermore, the modelling revealed a modest ~3% increase in Ac and an ~14% in NUE was accompanied when [Chl] reduced by 60%. However, if the leaf nitrogen conserved by this decrease in leaf [Chl] were to be optimally allocated to other components of photosynthesis, both Ac and NUE can be increased by over 30%. Optimizing [Chl] coupled with strategic reinvestment of conserved nitrogen is shown to have the potential to support substantial increases in Ac , biomass production, and crop yields.

[Protection and Mechanism of Qingyuan Shenghua Decoction on Multiple Organs of Sepsis Patients after Bone Trauma].

OBJECTIVE: To observe the protection of Qingyuan Shenghua Decoction (QSD) on multiple organs of sepsis patients after bone trauma, and to preliminarily explore its mechanism. METHODS: Totally 60 sepsis patients after bone trauma were randomly assigned to the treatment group and the control group according to random digit table, 30 in each group. All patients received routine Western medical treatment. Patients in the treatment group additionally took QSD or were nasally fed with QSD, one dose per day for 1 week. Changes of WBC, oxygenation index (PaO2/FiO2), serum creatinine (SCr), total bilirubin (TBIL), aspartate aminotransferase (AST), fibrinogen (FIB), D-dimer (DD), activated partial thromboplastin time (APTT), pro-calcitonin (PCT), C-reactive protein (CRP), heart rate (HR), mean arterial pressure (MAP), intra-abdominal pressure, scores for Acute Physiology and Chronic Health Evaluation II (APACHE II), sequential organ failure assessment (SOFA) scores were observed before treatment and on day 1, 3 and 7 after treatment. RESULTS: Compared with the control group at the same time point, MAP increased at post-treatment day 1 and 3; CRP, APTT, HR, SCr, TBIL, AST, intra-abdominal pressure at post-treatment day 3 obviously decreased in the treatment group (P < 0.05, P < 0.01). WBC, SOFA scores, PCT, CRP, APACHE II, APTT, D-D, HR, SCr, TBIL, AST and intra-abdominal pressure significantly decreased; FIB, MAP and PaO2/FiO2 obviously increased at post-treatment day 7 (P < 0.05, P < 0.01). CONCLUSION: QSD had good protective effect on multiple organ function in sepsis patients after bone trauma, and its mechanism might be related with effectively clearing endotoxin, alleviating inflammatory reactions, and fighting against coagulation dysfunction.

ER71 directs mesodermal fate decisions during embryogenesis.

Er71 mutant embryos are nonviable and lack hematopoietic and endothelial lineages. To further define the functional role for ER71 in cell lineage decisions, we generated genetically modified mouse models. We engineered an Er71-EYFP transgenic mouse model by fusing the 3.9 kb Er71 promoter to the EYFP reporter gene. Using FACS and transcriptional profiling, we examined the EYFP(+) population of cells in Er71 mutant and wild-type littermates. In the absence of ER71, we observed an increase in the number of EYFP-expressing cells, increased expression of the cardiac molecular program and decreased expression of the hemato-endothelial program, as compared with wild-type littermate controls. We also generated a novel Er71-Cre transgenic mouse model using the same 3.9 kb Er71 promoter. Genetic fate-mapping studies revealed that the ER71-expressing cells give rise to the hematopoietic and endothelial lineages in the wild-type background. In the absence of ER71, these cell populations contributed to alternative mesodermal lineages, including the cardiac lineage. To extend these analyses, we used an inducible embryonic stem/embryoid body system and observed that ER71 overexpression repressed cardiogenesis. Together, these studies identify ER71 as a critical regulator of mesodermal fate decisions that acts to specify the hematopoietic and endothelial lineages at the expense of cardiac lineages. This enhances our understanding of the mechanisms that govern mesodermal fate decisions early during embryogenesis.

[Fine mapping of complex disease susceptibility loci].

Genome-wide association studies (GWAS) using single nucleotide polymorphism (SNP) markers have identified more than 3800 susceptibility loci for more than 660 diseases or traits. However, the most significantly associated variants or causative variants in these loci and their biological functions have remained to be clarified. These causative variants can help to elucidate the pathogenesis and discover new biomarkers of complex diseases. One of the main goals in the post-GWAS era is to identify the causative variants and susceptibility genes, and clarify their functional aspects by fine mapping. For common variants, imputation or re-sequencing based strategies were implemented to increase the number of analyzed variants and help to identify the most significantly associated variants. In addition, functional element, expression quantitative trait locus (eQTL) and haplotype analyses were performed to identify functional common variants and susceptibility genes. For rare variants, fine mapping was carried out by re-sequencing, rare haplotype analysis, family-based analysis, burden test, etc.This review summarizes the strategies and problems for fine mapping.

Measuring Canopy Gas Exchange Using CAnopy Photosynthesis and Transpiration Systems (CAPTS).

Canopy photosynthesis (Ac), rather than leaf photosynthesis, is critical to gaining higher biomass production in the field because the daily or seasonal integrals of Ac correlate with the daily or seasonal integrals of biomass production. The canopy photosynthesis and transpiration measurement system (CAPTS) was developed to enable measurement of canopy photosynthetic CO2 uptake, transpiration, and respiration rates. CAPTS continuously records the CO2 concentration, water vapor concentration, air temperature, air pressure, air relative humidity, and photosynthetic photon flux density (PPFD) inside the chamber, which can be used to derive CO2 and H2O fluxes of a canopy covered by the chamber. This system can also be used to measure the fluxes of greenhouse gases when integrating with CH4 and N2O analyzers. Here, we describe the protocol for using CAPTS to perform experiments on rice (Oryza sativa L.) in paddy field, wheat (Triticum aestivum L.) in upland field, and tobacco (Nicotiana tabacum L.) in pots.

Advancing Thermoelectric Performance of Bi2Te3 below 400 K.

Thermoelectric cooling devices utilizing Bi2Te3-based alloys have seen increased utilization in recent years. However, their thermoelectric performance remains inadequate within the operational temperature range (≤400 K), with limited research addressing this issue. In this study, we successfully modulated the carrier concentration of the sample through Te content reduction, consequently lowering the peak temperature of the zT value from 400 to 300 K. This led to a substantial enhancement in thermoelectric performance at room temperature (≤400 K). Furthermore, by doping with La, the electrical transport properties have been further optimized, and the lattice thermal conductivity has been effectively reduced at the same time; the average zT value was ultimately elevated from 0.69 to 0.9 within the temperature range of 300-400 K. These findings hold significant promise for enhancing the efficacy of existing thermoelectric cooling devices based on Bi2Te3-based alloys.

MADS1-regulated lemma and awn development benefits barley yield.

Floral organ shape and size in cereal crops can affect grain size and yield, so genes that regulate their development are promising breeding targets. The lemma, which protects inner floral organs, can physically constrain grain growth; while the awn, a needle-like extension of the lemma, creates photosynthate to developing grain. Although several genes and modules controlling grain size and awn/lemma growth in rice have been characterized, these processes, and the relationships between them, are not well understood for barley and wheat. Here, we demonstrate that the barley E-class gene HvMADS1 positively regulates awn length and lemma width, affecting grain size and weight. Cytological data indicates that HvMADS1 promotes awn and lemma growth by promoting cell proliferation, while multi-omics data reveals that HvMADS1 target genes are associated with cell cycle, phytohormone signaling, and developmental processes. We define two potential targets of HvMADS1 regulation, HvSHI and HvDL, whose knockout mutants mimic awn and/or lemma phenotypes of mads1 mutants. Additionally, we demonstrate that HvMADS1 interacts with APETALA2 (A-class) to synergistically activate downstream genes in awn/lemma development in barley. Notably, we find that MADS1 function remains conserved in wheat, promoting cell proliferation to increase awn length. These findings extend our understanding of MADS1 function in floral organ development and provide insights for Triticeae crop improvement strategies.

NRDE2 deficiency impairs homologous recombination repair and sensitizes hepatocellular carcinoma to PARP inhibitors.

To identify novel susceptibility genes for hepatocellular carcinoma (HCC), we performed a rare-variant association study in Chinese populations consisting of 2,750 cases and 4,153 controls. We identified four HCC-associated genes, including NRDE2, RANBP17, RTEL1, and STEAP3. Using NRDE2 (index rs199890497 [p.N377I], p = 1.19 × 10-9) as an exemplary candidate, we demonstrated that it promotes homologous recombination (HR) repair and suppresses HCC. Mechanistically, NRDE2 binds to the subunits of casein kinase 2 (CK2) and facilitates the assembly and activity of the CK2 holoenzyme. This NRDE2-mediated enhancement of CK2 activity increases the phosphorylation of MDC1 and then facilitates the HR repair. These functions are eliminated almost completely by the NRDE2-p.N377I variant, which sensitizes the HCC cells to poly(ADP-ribose) polymerase (PARP) inhibitors, especially when combined with chemotherapy. Collectively, our findings highlight the relevance of the rare variants to genetic susceptibility to HCC, which would be helpful for the precise treatment of this malignancy.

Quantifying Contributions of Different Factors to Canopy Photosynthesis in 2 Maize Varieties: Development of a Novel 3D Canopy Modeling Pipeline.

Crop yield potential is intrinsically related to canopy photosynthesis; therefore, improving canopy photosynthetic efficiency is a major focus of current efforts to enhance crop yield. Canopy photosynthesis rate (Ac) is influenced by several factors, including plant architecture, leaf chlorophyll content, and leaf photosynthetic properties, which interact with each other. Identifying factors that restrict canopy photosynthesis and target adjustments to improve canopy photosynthesis in a specific crop cultivar pose an important challenge for the breeding community. To address this challenge, we developed a novel pipeline that utilizes factorial analysis, canopy photosynthesis modeling, and phenomics data collected using a 64-camera multi-view stereo system, enabling the dissection of the contributions of different factors to differences in canopy photosynthesis between maize cultivars. We applied this method to 2 maize varieties, W64A and A619, and found that leaf photosynthetic efficiency is the primary determinant (17.5% to 29.2%) of the difference in Ac between 2 maize varieties at all stages, and plant architecture at early stages also contribute to the difference in Ac (5.3% to 6.7%). Additionally, the contributions of each leaf photosynthetic parameter and plant architectural trait were dissected. We also found that the leaf photosynthetic parameters were linearly correlated with Ac and plant architecture traits were non-linearly related to Ac. This study developed a novel pipeline that provides a method for dissecting the relationship among individual phenotypes controlling the complex trait of canopy photosynthesis.

Lead-free and scalable GeTe-based thermoelectric module with an efficiency of 12.

GeTe-based materials with superior thermoelectric properties promise great potential for waste heat recovery. However, the lack of appropriate diffusion barrier materials (DBMs) limits not only the energy conversion efficiency but also the service reliability of the thermoelectric devices. Here, we propose a design strategy based on phase equilibria diagrams from first-principles calculations and identify transition metal germanides (e.g., NiGe and FeGe2) as the DBMs. Our validation experiment confirms the excellent chemical and mechanical stabilities of the interfaces between the germanides and GeTe. We also develop a process for scaling up the GeTe production. Combining with module geometry optimization, we fabricate an eight-pair module using mass-produced p-type Ge0.89Cu0.06Sb0.08Te and n-type Yb0.3Co4Sb12 and achieve a record-high efficiency of 12% among all reported single-stage thermoelectric modules. Our work thus paves the way for waste heat recovery based on completely lead-free thermoelectric technology.

Drosha processing controls the specificity and efficiency of global microRNA expression.

microRNAs (miRNAs) are a large family of approximately 22-nucleotide-long RNAs that regulate gene expression. They are first transcribed as long, primary transcripts, which then undergo a series of processing steps to generate the single-stranded, mature miRNAs. Here, we showed that Drosha cleaved hundreds of human primary miRNA transcript substrates with different efficiencies in vitro. The differential Drosha susceptibility of the primary miRNA transcripts significantly correlated with the expression of the corresponding, mature miRNAs in vivo. Conserved miRNAs were more efficiently expressed in vivo, and their primary transcripts were also better Drosha substrates in vitro. Combining secondary structure prediction and statistical analyses, we identified features in human primary miRNA transcripts that predisposed miRNAs to efficient Drosha processing in vitro as well as to better expression in vivo. We propose that the selectivity of Drosha action contributes greatly to the specificity and efficiency of miRNA biogenesis. Moreover, this study serves as an example of substrate specificity of a biochemical reaction regulating gene expression at a global scale in vivo. This article is part of a Special Issue entitled: MicroRNA's in viral gene regulation.