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Biology subjects

Luo, H.

Publications and source records attributed to Luo, H..

At least 109 records · Page 6Linked to original sources

Small volume blood-brain barrier opening in macaques with a 1 MHz ultrasound phased array

Focused ultrasound blood-brain barrier (BBB) opening is a promising tool for targeted delivery of therapeutic agents into the brain. The volume of opening determines the extent of therapeutic administration and sets a lower bound on the size of targets which can be selectively treated. We tested a custom 1 MHz array transducer optimized for cortical regions in the macaque brain with the goal of achieving small volume openings. We integrated this device into a magnetic resonance image guided focused ultrasound system and demonstrated twelve instances of small volume BBB opening with average opening volumes of 59 {+/-} 37 mm3 and 184 {+/-} 2 mm3 in cortical and subcortical targets, respectively. We developed real-time cavitation monitoring using a passive cavitation detector embedded in the array and characterized its performance on a bench-top flow phantom mimicking transcranial BBB opening procedures. We monitored cavitation during in-vivo procedures and compared cavitation metrics against opening volumes and safety outcomes measured with FLAIR and susceptibility weighted MR imaging. Our findings show small BBB opening at cortical targets in macaques and characterize the safe pressure range for 1 MHz BBB opening. Additionally, we used subject-specific simulations to investigate variance in measured opening volumes and found high correlation (R2 = 0.8577) between simulation predictions and observed measurements. Simulations suggest the threshold for 1 MHz BBB opening was 0.53 MPa. This system enables BBB opening for drug delivery and gene therapy to be targeted to more specific brain regions.

bioengineering↗

Regional and age-dependent changes in ubiquitination in cellular and mouse models of Spinocerebellar ataxia type 3

1Spinocerebellar ataxia type 3 (SCA3), also known as Machado-Joseph disease, is the most common dominantly inherited ataxia. SCA3 is caused by a CAG repeat expansion in the ATXN3 gene that encodes an expanded tract of polyglutamine (polyQ) in the disease protein ataxin-3 (ATXN3). As a deubiquitinating enzyme, ATXN3 regulates numerous cellular processes including proteasome- and autophagy-mediated protein degradation. In SCA3 disease brain, polyQ-expanded ATXN3 accumulates with other cellular constituents, including ubiquitin (Ub)-modified proteins, in select areas like the cerebellum and the brainstem, but whether pathogenic ATXN3 affects the abundance of ubiquitinated species is unknown. Here, in mouse and cellular models of SCA3, we investigated whether elimination of murine Atxn3 or expression of wild-type or polyQ-expanded human ATXN3 alters soluble levels of overall ubiquitination, as well as K48-linked (K48-Ub) and K63-linked (K63-Ub) chains. Levels of ubiquitination were assessed in the cerebellum and brainstem of 7- and 47-week-old Atxn3 knockout and SCA3 transgenic mice, and also in relevant mouse and human cell lines. In older mice, we observed that wild-type ATXN3 impacts the cerebellar levels of K48-Ub proteins. In contrast, pathogenic ATXN3 leads to decreased brainstem abundance of K48-Ub species in younger mice and changes in both cerebellar and brainstem K63-Ub levels in an age-dependent manner: younger SCA3 mice have higher levels of K63-Ub while older mice have lower levels of K63-Ub compared to controls. Human SCA3 neuronal progenitor cells also show a relative increase in K63-Ub proteins upon autophagy inhibition. We conclude that wild-type and mutant ATXN3 differentially impact K48-Ub- and K63-Ub-modified proteins in the brain in a region- and age-dependent manner.

neuroscience↗

USP39 promotes hepatocellular carcinogenesis through regulating alternative splicing in cooperation with SRSF6/HNRNPC

Abnormal alternative splicing (AS) caused by alterations in spliceosomal factors is implicated in cancers. Standard models posit that splice site selection is mainly determined by early spliceosomal U1, U2 snRNPs. Whether and how other mid/late-acting spliceosome components such as USP39 modulate tumorigenic splice site choice remain largely elusive. We observed that hepatocyte-specific knock-in of USP39 promoted hepatocarcinogenesis and potently regulated splice site selection. In human liver cancer cells, USP39 promoted tumor proliferation in a spliceosome-dependent manner. USP39 depletion deregulated hundreds of AS events, including the oncogenic splice-switching of KANK2. Mechanistically, we developed a novel RBP-motif enrichment analysis and found that USP39 modulated exon inclusion/exclusion by interacting with SRSF6/HNRNPC in both humans and mice. Our data represent a paradigm for the control of splice site selection by mid/late-acting spliceosome proteins and their interacting RBPs. USP39 and possibly other mid/late-acting spliceosome proteins may represent potential prognostic biomarkers and targets for cancer therapy. Graphic Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=97 SRC="FIGDIR/small/525324v1_ufig1.gif" ALT="Figure 1"> View larger version (32K): org.highwire.dtl.DTLVardef@34cbc1org.highwire.dtl.DTLVardef@2d0ee2org.highwire.dtl.DTLVardef@2c4bd6org.highwire.dtl.DTLVardef@26db00_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

Changes of platelet morphology, ultrastructure and function in patients with acute ischemic stroke based on super-resolution microscopy.

Platelets are important in acute ischemic stroke (AIS) thrombosis. The observation and evaluation of platelet ultrastructure and efficacy of antiplatelet drug in AIS patients is difficult due to microscopic limitations and sensitivity of platelet. The new super-resolution microscope (SIM) can accurately, quickly analyze the platelet ultrastructure and antiplatelet drug in AIS patients. We applied SIM to observe the morphology and ultrastructure of platelets with AIS patients in different state. SIM images were analyzed to specify the dense granules and granules change of platelets in AIS patients. Testing platelet factor 4 (PF4) to reflect platelet releasing function. We observed that platelet activation in AIS patients was greater after stimulation, with granule showing a pattern of parenchymatous masses. SIM images analyzing showed diameter of platelets, average size of granules, area% of granules per field and mean area of granules per platelet in AIS patient were lower than healthy people. Platelet releasing function was suppressed at rest stage and more efficacy release after stimulation. 2MeSamp inhibited parenchymatous masses of granules and reduced PF4 release of platelets after stimulation. According to the results, the structure and function of platelets in AIS patients are indeed altered. Additionally, SIM could be used as a new method to indicates the onset of AIS and assess antiplatelet drugs.

cell biology↗

Host transcriptome and microbiomeinteractions in Holstein cattle under heatstress condition

Climate changes affects animal physiology. In particular, rising ambient temperatures reduce animal vitality due to heat stress and this can be observed at various levels which included genome, transcriptome, and microbiome. In a previous study, microbiota highly associated with changes in cattle physiology were identified under heat stress conditions which included rectal temperature, drooling score, and respiratory score. In the present study, genes differentially expressed between individuals were selected representing different additive genetic effects towards the heat stress response in cattle in their production condition. Moreover, a correlation network analysis was performed to identify interactions between the transcriptome and microbiome for 71 Chinese Holstein cows sequenced for mRNA from blood samples and for 16S rRNA genes from fecal samples. Bioinformatics analysis was performed comprising: i) clustering and classification of 16S rRNA sequence reads, ii) mapping cows transcripts to the reference genome and their expression quantification, and iii) statistical analysis of both data types - including differential gene expression analysis and gene set enrichment analysis. A weighted co-expression network analysis was carried out to assess changes in the association between gene expression and microbiota abundance as well as to find hub genes/microbiota responsible for the regulation of gene expression under heat stress. Results showed 1,851 differentially expressed genes were found that were shared by three heat stress phenotypes. These genes were predominantly associated with the cytokine-cytokine receptor interaction pathway. The interaction analysis revealed three modules of genes and microbiota associated with rectal temperature with which two hubs of those modules were bacterial species, demonstrating the importance of the microbiome in the regulation of gene expression during heat stress. Genes and microbiota from the significant modules can be used as biomarkers of heat stress in cattle.

bioinformatics↗

Cleavage of 14-3-3ϵ by the enteroviral 3C protease dampens RIG-I mediated antiviral signaling

Viruses have evolved diverse strategies to evade the host innate immune response and promote infection. The RIG-I-like-receptors RIG-I and MDA5 (RLRs) are antiviral factors that sense viral RNA and signal downstream via mitochondrial antiviral-signaling protein (MAVS) to activate type I interferon (IFN) expression. 14-3-3{varepsilon} is a key component of the RIG-I translocon complex that interacts with MAVS at the mitochondrial membrane; however, the exact role of 14-3-3{varepsilon} in this pathway is not well understood. In this study, we demonstrate that 14-3-3{varepsilon} is a direct substrate of both the poliovirus and coxsackievirus B3 (CVB3) 3C proteases (3Cpro), and that it is cleaved at Q236{downarrow}G237, resulting in the generation of N- and C-terminal fragments of 27.0 and 2.1 kDa, respectively. Expression of the N-terminal cleavage fragment in cells reduces IFNB mRNA production during poly(I:C) stimulation, thus suggesting an antagonistic effect in the presence of the endogenous 14-3-3{varepsilon} protein. The N-terminal 14-3-3{varepsilon} fragment does not interact with RIG-I in co-immunoprecipitation assays, nor can it facilitate RIG-I translocation to the mitochondria. Probing the intrinsically disordered C-terminal region identifies key residues responsible for RIG-I signaling. Finally, overexpression of the N-terminal fragment promotes CVB3 infection and influenza A virus (H1N1) RNA production and reduces IFNB mRNA production during infection. The strategic enterovirus 3Cpro-mediated cleavage of 14-3-3{varepsilon} antagonizes RIG-I signaling by disrupting critical interactions within the RIG-I translocon complex, thus contributing to evasion of the host antiviral response. Author SummaryHost antiviral factors work to sense virus infection through various mechanisms, including a complex signaling pathway known as the RIG-I like receptor (RLR) pathway. This pathway drives the production of antiviral molecules known as interferons, which are necessary to establish an antiviral state in the cellular environment. Key to this antiviral signaling pathway is the small chaperone protein 14-3-3{varepsilon}, which facilitates the delivery of a viral sensor protein, RIG-I, to the mitochondria. In this study, we show that the enteroviral 3C protease cleaves 14-3-3{varepsilon} during infection, rendering it incapable of facilitating this antiviral response. We also find that the cleavage fragment inhibits RIG-I signaling and promotes virus infection. Our findings reveal a novel viral strategy that restricts the antiviral host response and provides insights into the mechanisms underlying 14-3-3{varepsilon} function in RIG-I antiviral signaling.

microbiology↗

Ori-Finder 2022: A Comprehensive Web Server for Prediction and Analysis of Bacterial Replication Origins

The replication of DNA is a complex biological process that is essential for life. Bacterial DNA replication is initiated at genomic loci referred to as replication origins (oriCs). Integrating the Z-curve method, DnaA box distribution, and comparative genomic analysis, we developed a web server to predict bacterial oriCs in 2008 called Ori-Finder, which contributes to clarify the characteristics of bacterial oriCs. The oriCs of hundreds of sequenced bacterial genomes have been annotated in their genome reports using Ori-Finder and the predicted results have been deposited in DoriC, a manually curated database of oriCs. This has facilitated large-scale data mining of functional elements in oriCs and strand-biased analysis. Here, we describe Ori-Finder 2022 with updated prediction framework, interactive visualization module, new analysis module, and user-friendly interface. More species-specific indicator genes and functional elements of oriCs are integrated into the updated framework, which has also been redesigned to predict oriCs in draft genomes. The interactive visualization module displays more genomic information related to oriCs and their functional elements. The analysis module includes regulatory protein annotation, repeat sequence discovery, homologous oriC search, and strand-biased analyses. The redesigned interface provides additional customization options for oriC prediction. Ori-Finder 2022 is freely available at http://tubic.tju.edu.cn/Ori-Finder2022 and https://tubic.org/Ori-Finder2022.

bioinformatics↗

Characterization and Preclinical Treatment of Rotational Force-Induced Brain Injury

Millions of traumatic brain injuries (TBIs) occur annually. TBIs commonly result from falls, traffic accidents, and sports-related injuries, all of which involve rotational acceleration/deceleration of the brain. During these injuries, the brain endures a multitude of primary insults including compression of brain tissue, damaged vasculature, and diffuse axonal injury. All of these deleterious effects can contribute to secondary brain ischemia, cellular death, and neuroinflammation that progress for weeks to months after injury and impede neurological recovery. While the linear effects of head trauma have been extensively modeled, less is known about how rotational injuries mediate neuronal damage following injury. Here, we developed a new model of rotational head trauma in rodents and extensively characterized the pathological, behavioral, and electrophysiological effects of rotational TBI (rTBI). We identify aberrant cyclin dependent kinase 5 (Cdk5) activity as a principal mediator of rTBI and show pharmacological inhibition of Cdk5 reduces the cognitive and pathological consequences of injury. Finally, we utilize Cdk5-enriched phosphoproteomics to uncover potential downstream mediators of rTBI. These studies contribute meaningfully to our understanding of the mechanisms of rTBI and how they may be effectively treated.

neuroscience↗

A Novel Bacterial Speciation Process Observed in a Symbiotic Marine Population

Incomplete lineage sorting (ILS), where ancestral polymorphisms persist through rapid speciation, is a hallmark of eukaryotic radiations but undocumented in prokaryotes. We report ILS associated speciation in the globally distributed marine bacterium Sulfitobacter, analyzing 74 strains from 16 oceanic regions and 15 ecosystem types. Genomic analysis resolved over ten genetically monomorphic clades sharing near uniform whole genome divergence (average nucleotide identity {approx}95%). However, individual genes and even adjacent nucleotide sites support conflicting phylogenetic relationships among clades. The median length of nearly identical sequence blocks supporting alternative topologies is less than 50 base pairs, far shorter than typical adaptive cassettes. This within gene, site level discordance provides a diagnostic signature of ancestral polymorphism retention following rapid fragmentation, ruling out adaptive gene sweeps. Demographic inference places this radiation on a timescale of tens of millennia, 100 to 1,000 fold faster than eukaryotic ILS, and traces the clades to a hyper polymorphic, highly recombining ancestor. Neutral simulations show that transient mutation surges or population bottlenecks alone can generate this pattern, without adaptive selection or ecological partitioning. By bridging eukaryotic and prokaryotic speciation paradigms, our findings demonstrate that ILS, previously considered exclusive to sexual eukaryotes, can drive rapid, neutral diversification in bacteria, expanding the mechanisms known to generate prokaryotic biodiversity.

microbiology↗

Co-occurrence of past and present shifts current neural representations and mediates serial biases

The regularities of the world render an intricate interplay between past and present. Even across independent trials, current-trial perception can be automatically shifted by preceding trials, namely the serial bias. Meanwhile, the neural implementation of the spontaneous shift of present by past that operates on multiple features remains unknown. In two auditory categorization experiments with human electrophysiology recordings, we demonstrate that serial bias arises from the co-occurrence of past-trial neural reactivation and the neural encoding of current-trial features. The meeting of past and present shifts the neural representation of current-trial features and modulates serial bias behavior. Critically, past-trial features (i.e., pitch, category, motor response) that constitute an event-file keep their respective identities in working memory and are only reactivated by the corresponding features in the current trial, giving rise to dissociated feature-specific serial biases. This event-file reactivation might constitute a fundamental mechanism for adaptive past-to-present generalizations over multiple features.

neuroscience↗

FBXO11 deficiency in mice impairs lung development and aggravates cigarette smoke-induced airway fibrosis

Small airway fibrosis is a common pathology of chronic obstructive pulmonary disease (COPD) and contributes to airflow obstruction. However, the underlying fibrogenic mechanism is poorly understood. Epithelial-mesenchymal transition (EMT) has been proposed as a driver of fibrosis. EMT occurs in the airways of COPD patients and smokers, but it remains elusive whether EMT may contribute to airway fibrosis. We previously reported that FBXO11 is a critical suppressor of EMT and Fbxo11 deficiency in mice causes neonatal lethality and EMT in epidermis. Here, we found that Fbxo11-deficient mouse embryonic lungs showed impaired epithelial differentiation, excess fibroblast cells surrounding the airways, and thickened interstitial mesenchyme. We further generated conditional mutant mice to ablate Fbxo11 selectively in the club airway epithelial cells in adult mice, which induced partial EMT in the airways. To determine the effect of EMT on airway fibrosis, Fbxo11 conditional mutant mice were exposed to cigarette smoke. Airway-specific loss of Fbxo11 markedly enhanced smoking-induced airway fibrotic remodeling and collagen deposition. Taken together, our study suggests that EMT in the airway epithelium exacerbates cigarette smoke-induced airway fibrosis.

cell biology↗

Dynamic emergence of relational structure network in human brains

Reasoning the hidden relational structure from sequences of events is a crucial ability humans possess, which help them to predict the future and make inferences. Besides simple statistical properties, humans also excel in learning more complex relational networks. Several brain regions are engaged in the process, yet the time-resolved neural implementation of relational structure learning and its behavioral relevance remains unknown. Here human subjects performed a probabilistic sequential prediction task on image sequences generated from a transition graph-like network, with their brain activities recorded using electroencephalography (EEG). We demonstrate the emergence of two key aspects of relational knowledge - lower-order transition probability and higher-order community structure, which arise around 840 msec after image onset and well predict behavioral performance. Furthermore, computational modeling suggests that the formed higher-order community structure, i.e., compressed clusters in the network, could be well characterized by a successor representation operation. Overall, human brains are constantly computing the temporal statistical relationship among discrete inputs, based on which new abstract knowledge could be inferred.

neuroscience↗

Systems analysis of metabolic responses to a mixed meal test in an obese cohort reveals links between tissue metabolism and the gut microbiota

Individuals with prediabetes and type 2 diabetes mellitus (T2DM) have poor ability to adapt to diet-triggered perturbations. We investigated global metabolic responses to a mixed meal test (MMT) in morbidly obese individuals with different diabetic status by performing plasma metabolomic profiling. Abnormal metabolism of carbohydrates, (branched-chain) amino acids, fatty acids and acylcholines in individuals with (pre)diabetes was observed. Moreover, differences in metabolic responses were associated with altered fecal metagenomics and transcriptomes of liver, jejunum and adipose tissues, which revealed a modified gut microbiome and multi-tissue metabolism in individuals having insulin resistance. Finally, using integrative machine learning models, we built a predictive model based on metabolomics data after 2h MMT, and identified possible new biomarkers for glycemic control including N-acetylaspartate and phenylalanine-derived metabolites that may be useful for diagnosis, intervention and prevention of T2DM.

systems biology↗

Reactivating ordinal position information from auditory sequence memory in human brains

Retaining a sequence of events in their order is a core ability of many cognitive functions, such as speech recognition, movement control, and episodic memory. Although content representations have been widely studied in working memory (WM), little is known about how ordinal position information of an auditory sequence is retained in the human brain as well as its coding characteristics. In fact, there is still a lack of an efficient approach to directly access the stored ordinal position code, since the neural activities enter a relatively activity-silent WM state during WM retention. Here participants performed an auditory sequence WM task with their brain activities recorded using electroencephalography (EEG). We developed new triggering events that could successfully reactivate neural representations of ordinal position from the activity-silent retention stage. Importantly, the rank reactivation is further related to recognition behavior, confirming its indexing of WM storage. Furthermore, the ordinal position code displays an intriguing stable-dynamic format, i.e., undergoing the same dynamic neutral trajectory during both encoding and retention (whenever reactivated). Overall, our results provide an effective approach to access the behaviorally-relevant ordinal position information in auditory sequence WM and reveal its new temporal characteristics.

neuroscience↗

Sparcl1/Hevin drives inflammatory and neuropathic pain through astrocyte and NMDA receptor signaling

Hevin/Sparcl1 is an astrocyte-secreted protein and regulates synapse formation in the brain. Here we show that astrocytic hevin signaling plays a critical role in maintaining chronic pain. Compared to wild-type mice, hevin-null mice exhibited normal mechanical and heat sensitivity but reduced inflammatory pain. Interestingly, hevin is required for the maintenance of nerve injury-induced neuropathic pain (mechanical allodynia), and hevin-null mice have faster recovery than wild-type mice from neuropathic pain after nerve injury. Intrathecal injection of wild-type hevin but not a hevin mutant that is no longer synaptogenic was sufficient to induce persistent mechanical allodynia in naive mice and further enhanced neuropathic pain in animals with nerve injury. In hevin-null mice with nerve injury, AAV-mediated re-expression of hevin, but not mutant hevin, in GFAP-expressing spinal cord astrocytes could reinstate neuropathic pain. Mechanistically, hevin is crucial for spinal cord NMDA receptor (NMDAR) signaling, as NMDA-induced mechanical allodynia and inward currents in spinal cord lamina II neurons is reduced in hevin-null mice. Hevin potentiated NMDA currents mediated by the GluN2B-containing NMDARs. Furthermore, intrathecal injection of a neutralizing antibody against hevin alleviated acute inflammatory pain and persistent neuropathic pain. Secreted hevin was detected in mouse cerebrospinal fluid (CSF) and nerve injury significantly increased CSF hevin abundance. Finally, neurosurgery caused rapid (< 10 hours) and substantial increases (~20 fold) in HEVIN levels in human CSF. Collectively, our findings support a critical role of hevin and astrocytes in the maintenance of chronic pain. Neutralizing of secreted hevin with monoclonal antibody may provide a new therapeutic strategy for treating chronic pain and NMDAR-medicated neurodegeneration.

neuroscience↗

Structure and function of diadenylate cyclase DacM from Mycoplasma ovipneumoniae

Cyclic diadenosine monophosphate (c-di-AMP) is a second-messenger nucleotide that is produced by many bacteria. C-di-AMP can not only regulate bacterial growth, cell-wall homeostasis, ion transport and gene transcription, but can also be recognized by multiple sensor / receptor proteins in infected host cells to trigger an innate immune response. Mycoplasma ovipneumoniae causes non-progressive pneumonia in both sheep and goats. Here, we analyzed c-di-AMP signaling in M. ovipneumoniae, which is a genome-reduced obligately pathogenic bacterium. Our results demonstrate that these bacteria can produce c-di-AMP, and we could identify the diadenylate cyclase, which was named DacM. The enzyme was found to utilize both ATP and ADP to synthesize c-di-AMP, resembling CdaM from a novel family of diadenylate cyclases first found in Mycoplasma pneumoniae. Furthermore, we present the crystal structures of DacM in the apo state and substrate-bound state at 3 [A] and 1.9 [A] resolution, respectively. Mutation of residues Asp112, Gly113, Tyr128, Phe129, and Arg143 surrounding the active sites to Ala were lethal to DacM enzymatic activity. These structures provide valuable insights into the biochemistry of c-di-AMP, and offer a basis for the structure-based design of new drugs for animal husbandry.

pathology↗

Lyophilized mRNA-lipid nanoparticles vaccine with long-term stability and high antigenicity against SARS-CoV-2

Advanced mRNA vaccines play vital roles against SARS-CoV-2. However, due to their poor stability, most current mRNA delivery platforms need to be stored at -20{degrees}C or -70{degrees}C, which severely limits their distribution. Herein, we present lyophilized SARS-CoV-2 mRNA-lipid nanoparticle vaccines, which can be stored at room temperature with long-term thermostability. In the in vivo Delta virus challenge experiment, lyophilized Delta variant mRNA vaccine successfully protected mice from infection and cleared the virus. Lyophilized omicron mRNA vaccine enabled to elicit both potent humoral and cellular immunity. In booster immunization experiments in mice and old monkeys, lyophilized omicron mRNA vaccine could effectively increase the titers of neutralizing antibodies against wild-type coronavirus and omicron variants. In humans, lyophilized omicron mRNA vaccine as a booster shot could also engender excellent immunity and had less severe adverse events. This lyophilization platform overcomes the instability of mRNA vaccines without affecting their bioactivity, and significantly improved their accessibility, particularly in remote regions.

immunology↗

Three-dimensional actuation of hummingbird wings requires diverse effects from the primary flight muscles

Hummingbirds have evolved to hover and maneuver with exceptional flight control. This is directly enabled by their musculoskeletal system that successfully exploits the agile motion of flapping wings. Here, we reveal novel principles of hummingbird wing actuation that provide insights into the evolution and robotic emulation of hummingbird flight. We develop a functional model of hummingbird musculoskeletal system, which predicts instantaneous, three-dimensional torque produced by primary (pectoralis and supracoracoideus) and combined secondary muscles. It also reveals primary muscle contractile behavior, including stress, strain, elasticity, and work. Results show that the primary muscles (i.e., the flight "engine") function as diverse effectors, as they do not simply power the stroke, but also actively deviate and pitch the wing. The secondary muscles produce controlled-tightening effects, by acting against primary muscles in deviation and pitching. The diverse effector capacity of pectoralis is associated with the evolution of a comparatively enormous bicipital crest on humerus.

biophysics↗