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1. A new phenological metric for use in pheno‐climatic models: A case study using herbarium specimens of Streptanthus tortuosus

   https://doi.org/10.1002/aps3.11276  

   Love, Natalie_L_Rossington; Park, Isaac_W; Mazer, Susan_J (July 2019, Applications in Plant Sciences)

   PremiseHerbarium specimens have been used to detect climate‐induced shifts in flowering time by using the day of year of collection (DOY) as a proxy for first or peak flowering date. Variation among herbarium sheets in their phenological status, however, undermines the assumption thatDOYaccurately represents any particular phenophase. Ignoring this variation can reduce the explanatory power of pheno‐climatic models (PCMs) designed to predict the effects of climate on flowering date. MethodsHere we present a protocol for the phenological scoring of imaged herbarium specimens using an ImageJ plugin, and we introduce a quantitative metric of a specimen's phenological status, the phenological index (PI), which we use inPCMs to control for phenological variation among specimens ofStreptanthus tortuosus(Brassicaceeae) when testing for the effects of climate onDOY. We demonstrate that includingPIas an independent variable improves model fit. ResultsIncludingPIinPCMs increased the modelR²relative toPCMs that excludedPI; regression coefficients for climatic parameters, however, remained constant. DiscussionOur protocol provides a simple, quantitative phenological metric for any observed plant. IncludingPIinPCMs increasesR²and enables predictions of theDOYof any phenophase under any specified climatic conditions. 

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2. Mediation of Cartilage Matrix Degeneration and Fibrillation by Decorin in Post‐traumatic Osteoarthritis

   https://doi.org/10.1002/art.41254  

   Li, Qing; Han, Biao; Wang, Chao; Tong, Wei; Wei, Yulong; Tseng, Wei‐Ju; Han, Li‐Hsin; Liu, X_Sherry; Enomoto‐Iwamoto, Motomi; Mauck, Robert_L; et al (July 2020, Arthritis & Rheumatology)

   ObjectiveTo elucidate the role of decorin, a small leucine‐rich proteoglycan, in the degradation of cartilage matrix during the progression of post‐traumatic osteoarthritis (OA). MethodsThree‐month–old decorin‐null (Dcn^−/−) and inducible decorin‐knockout (Dcn^iKO) mice were subjected to surgical destabilization of the medial meniscus (DMM) to induce post‐traumaticOA. TheOAphenotype that resulted was evaluated by assessing joint morphology and sulfated glycosaminoglycan (sGAG) staining via histological analysis (n = 6 mice per group), surface collagen fibril nanostructure via scanning electron microscopy (n = 4 mice per group), tissue modulus via atomic force microscopy–nanoindentation (n = 5 or more mice per group) and subchondral bone structure via micro–computed tomography (n = 5 mice per group). Femoral head cartilage explants from wild‐type and Dcn^−/−mice were stimulated with the inflammatory cytokine interleukin‐1β (IL‐1β) in vitro (n = 6 mice per group). The resulting chondrocyte response toIL‐1β and release ofsGAGs were quantified. ResultsIn both Dcn^−/−and Dcn^iKOmice, the absence of decorin resulted in acceleratedsGAGloss and formation of highly aligned collagen fibrils on the cartilage surface relative to the control (P< 0.05). Also, Dcn^−/−mice developed more salient osteophytes, illustrating more severeOA. In cartilage explants treated withIL‐1β, loss of decorin did not alter the expression of either anabolic or catabolic genes. However, a greater proportion ofsGAGs was released to the media from Dcn^−/−mouse explants, in both live and devitalized conditions (P< 0.05). ConclusionIn post‐traumaticOA, decorin delays the loss of fragmented aggrecan and fibrillation of cartilage surface, and thus, plays a protective role in ameliorating cartilage degeneration. 

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3. Hypoxia‐enhanced adhesion of red blood cells in microscale flow

   https://doi.org/10.1111/micc.12374  

   Kim, Myeongseop; Alapan, Yunus; Adhikari, Anima; Little, Jane A.; Gurkan, Umut A. (July 2017, Microcirculation)

   Abstract ObjectivesThe advancement of microfluidic technology has facilitated the simulation of physiological conditions of the microcirculation, such as oxygen tension, fluid flow, and shear stress in these devices. Here, we present a micro‐gas exchanger integrated with microfluidics to studyRBCadhesion under hypoxic flow conditions mimicking postcapillary venules. MethodsWe simulated a range of physiological conditions and exploredRBCadhesion to endothelial or subendothelial components (FNorLN). Blood samples were injected into microchannels at normoxic or hypoxic physiological flow conditions. Quantitative evaluation ofRBCadhesion was performed on 35 subjects with homozygousSCD. ResultsSignificant heterogeneity inRBCadherence response to hypoxia was seen amongSCDpatients.RBCs from a HEA population showed a significantly greater increase in adhesion compared toRBCs from a HNA population, for bothFNandLN. ConclusionsThe approach presented here enabled the control of oxygen tension in blood during microscale flow and the quantification ofRBCadhesion in a cost‐efficient and patient‐specific manner. We identified a unique patient population in whichRBCs showed enhanced adhesion in hypoxia in vitro. Clinical correlates suggest a more severe clinical phenotype in this subgroup. 

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4. A basic dd RAD seq two‐enzyme protocol performs well with herbarium and silica‐dried tissues across four genera

   https://doi.org/10.1002/aps3.11344  

   Jordon‐Thaden, Ingrid_E; Beck, James_B; Rushworth, Catherine_A; Windham, Michael_D; Diaz, Nicolas; Cantley, Jason_T; Martine, Christopher_T; Rothfels, Carl_J (April 2020, Applications in Plant Sciences)

   PremiseThe ability to sequence genome‐scale data from herbarium specimens would allow for the economical development of data sets with broad taxonomic and geographic sampling that would otherwise not be possible. Here, we evaluate the utility of a basic double‐digest restriction site–associatedDNAsequencing (ddRADseq) protocol usingDNAs from four genera extracted from both silica‐dried and herbarium tissue. MethodsDNAs fromDraba,Boechera,Solidago, andIlexwere processed with a ddRADseq protocol. The effects ofDNAdegradation, taxon, and specimen age were assessed. ResultsAlthough taxon, preservation method, and specimen age affected data recovery, large phylogenetically informative data sets were obtained from the majority of samples. DiscussionThese results suggest that herbarium samples can be incorporated into ddRADseq project designs, and that specimen age can be used as a rapid on‐site guide for sample choice. The detailed protocol we provide will allow users to pursue herbarium‐based ddRADseq projects that minimize the expenses associated with fieldwork and sample evaluation. 

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5. Beyond Autoantibodies: Biologic Roles of Human Autoreactive B Cells in Rheumatoid Arthritis Revealed by RNA‐Sequencing

   https://doi.org/10.1002/art.40772  

   Mahendra, Ankit; Yang, Xingyu; Abnouf, Shaza; Adolacion, Jay_R_T; Park, Daechan; Soomro, Sanam; Roszik, Jason; Coarfa, Cristian; Romain, Gabrielle; Wanzeck, Keith; et al (February 2019, Arthritis & Rheumatology)

   ObjectiveTo obtain the comprehensive transcriptome profile of human citrulline‐specific B cells from patients with rheumatoid arthritis (RA). MethodsCitrulline‐ and hemagglutinin‐specific B cells were sorted by flow cytometry using peptide–streptavidin conjugates from the peripheral blood ofRApatients and healthy individuals. The transcriptome profile of the sorted cells was obtained byRNA‐sequencing, and expression of key protein molecules was evaluated by aptamer‐basedSOMAscan assay and flow cytometry. The ability of these proteins to effect differentiation of osteoclasts and proliferation and migration of synoviocytes was examined by in vitro functional assays. ResultsCitrulline‐specific B cells, in comparison to citrulline‐negative B cells, from patients withRAdifferentially expressed the interleukin‐15 receptor α (IL‐15Rα) gene as well as genes related to protein citrullination and cyclicAMPsignaling. In analyses of an independent cohort of cyclic citrullinated peptide–seropositiveRApatients, the expression ofIL‐15Rα protein was enriched in citrulline‐specific B cells from the patients’ peripheral blood, and surprisingly, all B cells fromRApatients were capable of producing the epidermal growth factor ligand amphiregulin (AREG). Production ofAREGdirectly led to increased migration and proliferation of fibroblast‐like synoviocytes, and, in combination with anti–citrullinated protein antibodies, led to the increased differentiation of osteoclasts. ConclusionTo the best of our knowledge, this is the first study to document the whole transcriptome profile of autoreactive B cells in any autoimmune disease. These data identify several genes and pathways that may be targeted by repurposing severalUSFood and Drug Administration–approved drugs, and could serve as the foundation for the comparative assessment of B cell profiles in other autoimmune diseases. 

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