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Search indexed bioRxiv preprints in genomics, neuroscience, cell biology and bioinformatics. Read source abstracts and check manuscript versions; preprints are not peer reviewed.

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bioRxiv2018

High-throughput antibody engineering in mammalian cells by CRISPR/Cas9-mediated homology-directed mutagenesis

Antibody engineering is performed to improve therapeutic properties by directed evolution, usually by high-throughput screening of phage or yeast display libraries. Engineering antibodies in mammalian cells offers advantages associated with expression in their final therapeutic format (full-length glycosylated IgG), however, the inability to express large and diverse libraries severely limits their potential throughput. To address this limitation, we have developed homology-directed mutagenesis (HDM), a novel method which extends the concept of CRISPR/Cas9-mediated homology-directed repair (HDR). HDM leverages oligonucleotides with degenerate codons to generate site-directed mutagenesis libraries in mammalian cells. By improving HDM efficiency (>35-fold) and combining mammalian display screening with next-generation sequencing (NGS), we validated this approach can be used for key applications in antibody engineering at high-throughput: rational library construction, novel variant discovery, affinity maturation, and deep mutational scanning (DMS). We anticipate that HDM will be a valuable tool for engineering and optimizing antibodies in mammalian cells, and eventually enable directed evolution of other complex proteins and cellular therapeutics.

bioengineering↗

bioRxiv2018

An aged human heart tissue model showing age-related molecular and functional deterioration resembling the native heart

Deaths attributed to ischemic heart disease increased by 41.7% from 1990 to 2013. This is primarily due to an increase in the aged population, however, research on cardiovascular disease (CVD) has been overlooking aging, a well-documented contributor to CVD. The field heavily depends on the use of young animals due to lower costs and ready availability, despite the prominent differences between young and aged heart structure and function. Here we present the first human induced pluripotent stem cell (hiPSC)-derived cardiomyocyte (iCM)-based, in vitro aged myocardial tissue model as an alternative research platform. Within 4 months, iCMs go through accelerated senescence and show cellular characteristics of aging. Furthermore, the model tissues fabricated using these aged iCMs, with stiffness resembling that of aged human heart, show functional and pharmacological deterioration specific to aged myocardium. Our novel tissue model with age-appropriate physiology and pathology presents a promising new platform for investigating CVD or other age-related diseases.

bioengineering↗

bioRxiv2018

Engineered Peptide Barcodes for In-Depth Analyses of Binding Protein Ensembles

Binding protein generation relies on laborious screening cascades that process candidate molecules individually. To break with this paradigm, we developed NestLink, a binder selection and identification technology able to biophysically characterize thousands of library members at once without handling individual clones at any stage of the process. NestLink builds on genetically fused barcoding peptides, termed flycodes, which are designed for maximal detectability by mass spectrometry and serve as unique molecular identifiers for accurate deep sequencing. We applied NestLink to overcome current limitations of binder generation. Rare binders against an integral membrane protein were identified directly in the cellular environment of a human pathogen. Hundreds of binder candidates were simultaneously ranked according to kinetic parameters. Adverse effects of target immobilization were overcome by selecting nanobodies against an ABC transporter entirely in solution. NestLink may provide a basis for the selection of tailored binder characteristics directly in tissues or in living organisms.

bioengineering↗

bioRxiv2018

Low-Cost Touchscreen Driven Programmable Dual Syringe Pump for Life Science Applications

Syringe pumps are powerful tools able to automate routine laboratory practices that otherwise consume large amounts of manual labor time. Commercially available syringe pumps are expensive, difficult to customize, and often preset for a narrow range of operations. Here, we show how to build a programmable dual syringe pump (PDSP) that overcomes these limitations. The PDSP is driven by a Raspberry Pi paired with a stepper motor controller to allow maximal customization via Python scripting. The entire setup can be controlled by a touchscreen for use without a keyboard or mouse. Furthermore, the PDSP is structured around 3D printed parts, enabling users to change any component for their specific application. We demonstrate one application of the PDSP by using it to generate whole cell lysates using a cell homogenizer in an automated fashion.\n\nSpecifications table\n\nO_TBL View this table:\norg.highwire.dtl.DTLVardef@17fdadorg.highwire.dtl.DTLVardef@10f7536org.highwire.dtl.DTLVardef@1d854c6org.highwire.dtl.DTLVardef@1a5d4bcorg.highwire.dtl.DTLVardef@31ad8b_HPS_FORMAT_FIGEXP M_TBL C_TBL

bioengineering↗

bioRxiv2018

Competing endogenous RNA network: Potential entrants to gene editing in Hepatocellular Carcinoma

BackgroundHepatocellular Carcinoma (HCC) is the leading cause of cancer deaths worldwide as well as in Egypt. We aimed to use Clustered Regulatory Interspaced Short Palindromic Repeats (CRISPR) gene editing technique to induce forced down-regulation of the circRNA which consequently modified miRNA expression in HepG2 cell line to prove the regulatory relationship between the RNA parts of an in silico-detected competing endogenous RNA network in HCC\n\nMethodWe first retrieved hsa_circ_0000064-miR-1285-TRIM2 mRNA from public microarray databases followed by in silico modelling to mimic the regulation kinetics of cirRNA associated ceRNA network. Secondly, we performed polymerase chain reaction (PCR)-based amplification of synthetic fragments, Gibson assembly of both CRISPR and non CRISPR based circuits, E-coli transformation, plasmid purification, HePG2 cell line transfection. Finally Expression levels of the chosen RNAs in hepatocellular carcinoma (HCC) cell line, HepG2, were examined by quantitative reverse transcription polymerase chain reaction (qRT-PCR) and the cytotoxic effect was validated by viability assay.TRIM2 protein expression was proved by immunohistochemistry and flowcytometry.\n\nResultsInduction of hsa_circ_0000064 into HepG2 cell line via CRISPR-and non-CRISPR mediated synthetic circuit resulted in statistically significant decrease in cell number and, then, cellular viability with marked increase in hsa_circ_0000064 and TRIM2 mRNA levels and concomitant decrease in miR-1285 expression in HepG2 cell line compared with control (p<0.0). Moreover exogenous expression of hsa_circ_0000064 in HepG2 cell line showed increased expression of the tumor suppressor protein, TRIM2.\n\nConclusionsOur integrative approach, including in silico data analysis and experimental validation proved that CRISPR-mediated synthetic circuit-based overexpression of hsa_circ_0000064 was more efficient than conventional transient transfection, representing a promising therapeutic strategy for HCC.\n\nData AvailabilityOur Data was made available online on the IGEM wiki of team AFCM-EGYPT: http://2017.igem.org/Team:AFCM-Egypt. Synthetic parts have been submitted to IGEM Parts Registry.\n\nFinancial DisclosureThe project was funded by Armed Forces College of Medicine AFCM, Zewail City of Science and Technology, National Research Center NRC, VitaBiotics, PHARCO Pharmaceuticals, Sim Era and DANUB Paintings. IDT provided 20 kb of DNA synthesis. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

bioengineering↗

bioRxiv2018

Coupling initial hydrogel microenvironments with mesenchymal stem cell remodeling to define a dynamic hematopoietic stem cell niche

Hematopoietic stem cells (HSCs) reside in the bone marrow within discrete niches defined by a complex milieu of external signals including biophysical cues, bound and diffusible biomolecules, and heterotypic cell-cell interactions. Recent studies have shown the importance of autocrine-mediated feedback of cell-secreted signals and the interplay between matrix architecture and biochemical diffusion on hematopoietic stem cell activity. Autocrine and paracrine signaling from HSCs and niche-associated mesenchymal stromal cells (MSCs) have both been suggested to support HSC maintenance in vivo and in vitro. Here we report the development of a library of methacrylamide-functionalized gelatin (GelMA) hydrogels to explore the balance between autocrine feedback and paracrine signals from co-encapsulated murine bone marrow MSCs on murine HSCs. The use of a degradable GelMA hydrogel enables the possibility for significant MSC-mediated remodeling, yielding dynamic shifts in the matrix environment surrounding HSCs. We identify a combination of an initially low-diffusivity hydrogel and a 1:1 HSPC:MSC seeding ratio as conducive to enhanced HSC population maintenance and quiescence. Further, gene expression and serial mechanical testing data suggests that MSC-mediated matrix remodeling is significant for the long-term HSC culture, reducing HSC autocrine feedback and potentially enhancing MSC-mediated signaling over 7-day culture in vitro. This work demonstrates the design of an HSC culture system that couples initial hydrogel properties, MSC co-culture, and concepts of dynamic reciprocity mediated by MSC remodeling to achieve enhanced HSC maintenance. One Sentence SummaryCoupling effects of hydrogel biotransport, heterotypic cell culture, and matrix remodeling enhances hematopoietic stem cell culture and quiescence.

bioengineering↗

bioRxiv2018

Oblique plane single-molecule localization microscopy for thick samples

We introduce single-molecule oblique plane microscopy (obSTORM) to directly image oblique sections of thick samples into depth without lengthy axial stack acquisition. Using oblique light-sheet illumination and oblique fluorescence detection, obSTORM offers uniform super-resolution throughout imaging depth in diverse biological specimens from cells to tissues. In particular, we demonstrate an isotropic resolution of [~]51 nm over a depth of 32 m for a tissue sample, and comparable resolution over a depth of 100 m using fluorescent beads.

bioengineering↗

bioRxiv2018

Complete guide RNA design for CRISPR-mediated regulation of human long noncoding RNA transcription

Transcription inhibition and activation of long noncoding RNAs (lncRNAs) mediated by clustered regularly interspaced short palindromic repeat (CRISPR)/Cas9 technology provides potential advantages in high-throughput functional genomics studies over RNA interference or overexpression platforms. In this work, we identify over 90,000 lncRNA transcription start sites (TSSs) based on the MiTranscriptome human genome annotation and design single guide RNA (sgRNA) libraries with strong predicted activities and low off-target effects for CRISPR-mediated inhibition and activation (CRISPRi/a) of their transcription. A large fraction of these TSSs correspond to putative genes that are not annotated in common reference genome annotations and have never been functionally studied. Our CRISPRi/a libraries, or their context-dependent subsets, are potentially useful in genome-scale functional studies of human lncRNAs.

bioengineering↗

bioRxiv2018

Functional Deficits are Explained by Plantarflexor Remodeling Following Achilles Tendon Rupture Repair: Preliminary Findings

Achilles tendon ruptures are painful injuries that often lead to long-term functional deficits. Despite the prevalence of these injuries, the mechanism responsible for limited function has not yet been established. Therefore, the purpose of this study was to present preliminary findings that support a hypothesis that skeletal muscle remodeling is the driving factor of poor outcomes in some patients. Biomechanical and ultrasonography assessments were performed on a patient that presented with poor functional outcomes 2.5 years after a surgically-repaired acute Achilles tendon rupture. Single-leg heel raise function was decreased by 70% in the affected limb while walking mechanics showed no deficits. Ultrasonography revealed that the affected limb had shorter, more pennated, and less thick medial gastrocnemius muscles compared to the unaffected limb. A simple computational model of a maximal-effort plantarflexion contraction was employed to test the implications of muscle remodeling on single-leg heel raise function. Subject-specific fascicle length and pennation measurements explained deficits in ankle work and power that strongly agreed with experimentally measured values using motion capture. These preliminary findings support the hypothesis that skeletal muscle goes extensively remodels in response to a ruptured tendon, which reduces the amount of work and power the joint can generate. This multidisciplinary framework of biomechanical, imaging, and computational modeling provides a unique platform for studying the complex interactions between structure and function in patients recovering from Achilles tendon injuries.

bioengineering↗

bioRxiv2018

Achilles Tendon Structure Differs Between Runners And Non-Runners Despite No Clinical Signs Or Symptoms Of Mid-Substance Tendinopathy

Achilles tendinopathy affects many running athletes and often leads to chronic pain and functional deficits. While changes in tendon structure have been linked with tendinopathy, the effects of distance running on tendon structure is not well understood. Therefore, the purpose of this study was to characterize structural differences in the Achilles tendons in healthy young adults and competitive distance runners using quantitative ultrasound analyses. We hypothesized that competitive distance runners with no clinical signs or symptoms of tendinopathy would have quantitative signs of tendon damage, characterized by decreased collagen alignment and echogenicity, in addition to previous reports of thicker tendons. Longitudinal ultrasound images of the right Achilles tendon mid-substance were acquired in competitive distance runners and recreationally-active adults. Collagen organization, mean echogenicity, and tendon thickness were quantified using image processing techniques. Clinical assessments confirmed that runners had no signs or symptoms of tendinopathy and controls were only included if they had no history of Achilles tendon pain or injuries. Runner tendons were 40% less organized, 48% thicker, and 41% less echogenic compared to the control tendons (p < 0.001). Young adults engaged in competitive distance-running have structurally different tendons than recreationally-active young adults. While these structural differences have been associated with tendon damage, the lack of clinical symptoms of tendinopathy may suggest that these detected differences may either be precursors of tendinopathy development or protective adaptations to cyclic tendon loading experienced during running.

bioengineering↗

bioRxiv2018

The Impact Of Thigh And Shank Marker Quantity On Lower Extremity Kinematics Using A Constrained Model

Musculoskeletal models are commonly used to quantify joint motions and loads during human motion. Constraining joint kinematics simplifies these models but the implications of the number of markers used during data acquisition remains unclear. The purpose of this study was to establish the effects of marker placement and quantity on kinematic fidelity when using a constrained-kinematic model. We hypothesized that a constrained-kinematic model would faithfully reproduce lower extremity kinematics regardless of the number of tracking markers removed from the thigh and shank. Healthy-young adults (N = 10) walked on a treadmill at slow, moderate, and fast speeds while skin-mounted markers were tracked using motion capture. Lower extremity kinematics were calculated for 256 combinations of leg and shank markers to establish the implications of marker placement and quantity on joint kinematics. Sagittal joint and hip coronal kinematics errors were smaller than documented errors caused by soft-tissue artifact, which tends to be approximately 5 degrees, when excluding thigh and shank markers. Joint angle and center kinematic errors negatively correlated with the number of markers included in the analyses (R2 > 0.97) and typically showed the greatest error reductions when two markers were included. Further, we demonstrated that a simplified marker set that included markers on the pelvis, lateral knee condyle, lateral malleolus, and shoes produced kinematics that strongly agreed with the traditional marker set. In conclusion, constrained-kinematic models are resilient to marker placement and quantity, which has implications on study design and post-processing workflows.\n\nEthics Approval and Consent to Participate this study was approved by the Institutional Review Board at the University of Pennsylvania (#824466). Subjects provided written-informed consent\n\nConsent to Publish this submission does not contain any individual data\n\nAvailability of Data and Materials the datasets analyzed in this study are available from the corresponding author on reasonable request.\n\nCompeting Interests one author (JB) is an associate editor for BMC Musculoskeletal Disorders. None of the other authors have any competing interests.\n\nFunding no funding has been provided for this research\n\nAuthors ContributionsAS, TH, and JB designed the experiment; AS and TH collected the data; AS and JB analyzed and interpreted the data; AS and JB drafted the manuscript; AS, TH, and JB revised the intellectual content of the manuscript; AS, TH, and JB approved the final version of the manuscript; and AS, TH, and JB agreed to be accountable for all aspects of the study.

bioengineering↗

bioRxiv2018

Plantarflexor Moment Arms Estimated From Tendon Excursion In Vivo Are Not Well Correlated With Geometric Measurements

Geometric and tendon excursion methods have both been used extensively for estimating plantarflexor muscle moment arm in vivo. Geometric measures often utilize magnetic resonance imaging, which can be costly and impractical for many investigations. Estimating moment arm from tendon excursion measured with ultrasonography may provide a cost-effective alternative to geometric measures of moment arm, but how well such measures represent geometry-based moment arms remains in question. The purpose of this study was to determine whether moment arms from tendon excursion can serve as a surrogate for moment arms measured geometrically. Magnetic resonance and ultrasound imaging were performed on 19 young male subjects to quantify plantarflexor moment arm based on geometric and tendon excursion paradigms, respectively. These measurements were only moderately correlated (R2 = 0.21, p = 0.052), and moment arm from tendon excursion under-approximated geometric moment arm by nearly 40% (p < 0.001). This moderate correlation between methods is at odds with a prior report (N = 9) of a very strong correlation (R2 = 0.94) in a similar study. Therefore, we performed 92,378 regression analyses (19 choose 9) to determine if such a strong correlation existed in our study population. We found that certain sub-populations of the current study generated similarly strong coefficients of determination (R2 = 0.92), but 84% of all analyses revealed no correlation (p > 0.05). Our results suggest that the moment arms from musculoskeletal geometry cannot be otherwise obtained by simply scaling moment arms estimated from tendon excursion.

bioengineering↗

bioRxiv2018

A new approach to design artificial 3D micro-niches with combined chemical, topographical and rheological cues

The in vitro methods to recapitulate environmental cues around cells are usually optimized to test a specific property of the environment (biochemical nature or the stiffness of the extra cellular matrix (ECM), or nanotopography) for its capability to induce defined cell behaviors (lineage commitment, migration). Approaches that combine different environmental cues in 3D to assess the biological response of cells to the spatial organization of different biophysical and biochemical cues are growingly being developed. We demonstrate how the lamination of through-hole polymeric bio-functionalized membranes can be implemented to create complex bona fide micro-niches with differential 3D environmental properties using photoactive materials. Our approach enables to create micro-niches ranging in size from single cells to cell aggregates. They are bio-functionalized in 3D simultaneously with topographical featured, protein patterns and structured ECM surrogate with 1 micrometer resolution. We demonstrate how these niches extend in 3D the ability to pattern cells. We exemplify how they can be used to standardize cells shapes in 3D and to trigger the apico-basal polarization of single epithelial cells.

bioengineering↗

bioRxiv2018

Influence of hyaluronic acid transitions in tumor microenvironment on glioblastoma malignancy and invasive behavior

The extracellular matrix (ECM) is critical in tumor growth and invasive potential of cancer cells. In glioblastoma tumors, some components of the native brain ECM such as hyaluronic acid (HA) have been suggested as key regulators of processes associated with poor patient outlook such as invasion and therapeutic resistance. Given the importance of cell-mediated remodeling during invasion, it is likely that the molecular weight of available HA polymer may strongly influence GBM progression. Biomaterial platforms therefore provide a unique opportunity to systematically examine the influence of the molecular weight distribution of HA on GBM cell activity. Here we report the relationship between the molecular weight of matrix-bound HA within a methacrylamide-functionalized gelatin (GelMA) hydrogel, the invasive phenotype of a patient-derived xenograft GBM population that exhibits significant in vivo invasivity, and the local production of soluble HA during GBM cell invasion. Hyaluronic acid of different molecular weights spanning a range associated with cell-mediated remodeling (10, 60, and 500 kDa) was photopolymerized into GelMA hydrogels, with cell activity compared to GelMA only conditions (-HA). Polymerization conditions were tuned to create a homologous series of GelMA hydrogels with conserved poroelastic properties (i.e. shear modulus, Poissons ratio, and diffusivity). GBM migration was strongly influenced by HA molecular weight. While markers associated with active remodeling of the HA content, hyaluronan synthase and hyaluronidase, were found to be insensitive to matrix immobilized HA content. These results provide new information regarding the importance of local hyaluronic acid content on the invasive phenotype of GBM.

bioengineering↗

bioRxiv2018

Age dependence of systemic bone loss and recovery following femur fracture in mice

The most reliable predictor of future fracture risk is a previous fracture of any kind. The etiology of this increased fracture risk is not fully known, but it is possible that fracture initiates systemic bone loss leading to greater fracture risk at all skeletal sites. In this study we investigated systemic bone loss and recovery following femoral fracture in young (3 month old) and middle-aged (12 month old) mice. Transverse femur fractures were created using a controlled impact, and whole-body bone mineral density (BMD), trabecular and cortical microstructure, bone mechanical properties, bone formation and resorption rates, mouse voluntary movement, and systemic inflammation were quantified at multiple time points post-fracture. We found that fracture led to decreased whole-body BMD in both young and middle-aged mice 2 weeks post-fracture; this bone loss was recovered by 6 weeks in young, but not middle-aged mice. Similarly, trabecular bone volume fraction (BV/TV) of the L5 vertebral body was significantly reduced in fractured mice relative to control mice 2 weeks post-fracture (-11% for young mice, -18% for middle-aged mice); this bone loss was fully recovered by 6 weeks post-fracture in young mice. At 3 days post-fracture we observed significant increases in serum levels of interleukin-6 and significant decreases in voluntary movement in fractured mice compared to control mice, with considerably greater changes in middle-aged mice than in young mice. At this time point we also observed increased osteoclast number on L5 vertebral body trabecular bone of fractured mice compared to control mice. These data show that systemic bone loss occurs after fracture in both young and middle-aged mice, and recovery from this bone loss may vary with age. This systemic response could contribute to increased future fracture risk following fracture, and these data may inform clinical treatment of fractures with respect to improving long-term skeletal health.

bioengineering↗

bioRxiv2018

Short cracks in knee meniscus tissue cause strain concentrations, but not weakness, in single-cycle uniaxial tension

Tears are central to knee meniscus pathology and, from a mechanical perspective, are crack-like defects (cracks). In many materials, cracks create stress concentrations that cause progressive local rupture and reduce effective strength. It is currently un-known if cracks in meniscus have these consequences; if they do, this would have repercussions for management of meniscus pathology. The objective of this study was to determine if a short crack in meniscus tissue, which mimics a preclinical meniscus tear, (a) causes crack growth and reduces effective strength, (b) creates a near-tip strain concentration, and (c) creates unloaded regions on either side of the crack. Specimens with and without cracks were tested in uniaxial tension and compared in terms of macroscopic stress-strain curves and digital image correlation strain fields. The strain fields were used as an indicator of stress concentrations and unloaded regions. Effective strength was found to be insensitive to the presence of a crack (potential effect < 0.86 s.d.; {beta} = 0.2), but significant strain concentrations, which have the potential to lead to long-term accumulation of tissue or cell damage, were observed near the crack tip.

bioengineering↗

bioRxiv2018

Systemically administered MSCs given 24hrs after osteotomy do not affect bone formation in rat distraction osteogenesis

Distraction osteogenesis is a unique postnatal bone formation employed by orthopaedic surgeons to treat many conditions, however, the overall time to external frame removal can be extensive. Any strategies that accelerate healing would improve patient care. Distraction osteogenesis research in the past decade has shown that direct stem cell implantation enhances new bone formation. Systemic implantation would be more clinically desirable. Systemically delivered stem cells have been shown to home to a mandibular distraction site; however, effects on bone formation have not been studied. Ten-week-old, male Sprague-Dawley rats underwent surgery to implant an external fixator-distractor and an osteotomy was performed. Twenty-four hours postoperatively, each rat received tail vein injections of either saline or 10^6 fluorescently labeled primary mesenchymal stem cells. Animals in the validation groups were euthanized two days after surgery and the femora processed for histology. Animals in the experimental groups were given five days of latency, then the femur was lengthened once daily for five days (0.75mm/day, 3.75mm total). Following four weeks of consolidation, the animals were euthanized and the femora were evaluated by microCT and histology to quantify new bone formation. Labeled stem cells were found at the distraction site in validation animals. However, there were no differences in any bone or soft tissue outcomes. Systemic stem cell administration 24 hours after surgery does not improve DO outcomes. It is possible that the animal model was not challenging enough to discriminate any augmentation provided by stem cells.

bioengineering↗

bioRxiv2018

Integrative visual omics of the white-rot fungus Polyporus brumalis exposes the biotechnological potential of its oxidative enzymes for delignifying raw plant biomass.

White-rot fungi are wood decayers able to degrade all polymers from lignocellulosic biomass including cellulose, hemicelluloses, and lignin. The white-rot fungus Polyporus brumalis efficiently breaks down lignin and is regarded as having a high potential for the initial treatment of plant biomass in its conversion to bio-energy. We performed integrative multi-omics analyses by combining data from the fungal genome, transcriptomes, and secretomes. We found the fungus possessed an unexpectedly large set of genes coding for enzymes related to lignin degradation, and that these were highly expressed and massively secreted under solid-state fermentation conditions. The examination of interrelated multi-omics patterns revealed the coordinated regulation of lignin-active peroxidases and H2O2-generating enzymes along with the activation of cellular mechanisms for detoxification, which combined to result in the efficient lignin breakdown by the fungus.\n\nImportancePlant biomass conversion for green chemistry and bio-energy is a current challenge for a modern sustainable bioeconomy. The complex polyaromatic lignin polymers in raw biomass feedstocks (i.e. agriculture and forestry by-products) are major obstacles for biomass conversions. From a biotechnological aspect, these compounds could be a potential source of aromatic platform molecules for bio-based polymers. Here we describe the extraordinary ability of Polyporus brumalis for lignin degradation using its enzymatic arsenal to break down wheat straw, a lignocellulosic substrate that is considered as a biomass feedstock worldwide. We observed unusual expansions of gene families coding for; 1) Class II peroxidases involved in lignin degradation; and 2) GMC oxidoreductases/dehydrogenases involved in generating the hydrogen peroxide required for lignin peroxidase activity. Our findings suggested the fungus massively mobilizes this oxidative machinery during growth on wheat straw. Overall, we identified sets of co-regulated enzymes, which could potentially augment the efficiency of biotechnological plant biomass conversions.

bioengineering↗