Biofabrication of neural microphysiological systems using magnetic spheroid bioprinting

The high attrition rate of neuro-pharmaceuticals as they proceed to market necessitates the development of clinically-relevant in vitro neural microphysiological systems that can be utilized during the preclinical screening phase to assess the safety and efficacy of potential compounds. Historically, proposed models have adhered to two distinct approaches; those that are biologically relevant (e.g.-organoids, spheroids) or those that provide engineering control (e.g.-bioprinting, microfluidics). Separately, these approaches fail to fully recapitulate the complex hierarchical structure of the nervous system, limiting their clinical applications. Furthermore, the reliance on manual implementation present in many models fails to effectively scale up or satisfy the consistency standards required for widespread industry adoption. This work serves as a proof-of-concept for merging the two approaches to create a neural microphysiological system that overcomes their individual limitations. Spinal cord spheroids, fabricated using magnetic nanoparticles, are positioned in a three-dimensional hydrogel construct using magnetic bioprinting. Resulting constructs demonstrate both localized cell-cell interactions and long-distance projections that mimic in vivo structure. The use of magnetic nanoparticles for spheroid formation provides batch-to-batch consistency in size and shape and reduces the reliance on trained experimenters for accurate placing for culture. Taken together, this combination approach provides the first steps towards developing a simple approach for integrating spheroid, hydrogel culture, and bioprinting as an alternative to more specialized and expensive processes.

Determination of cell nucleus-to-cytoplasmic ratio using imaging flow cytometry and a combined ultrasound and photoacoustic technique: a comparison study

While the nucleus-to-cytoplasmic (N:C) ratio has traditionally been used for assessing cell malignancy, most N:C measurement techniques are time-consuming and performed on thin histological sections, which prohibit assessment of three-dimensional cell structure. A combined ultrahigh frequency ultrasound (US) and photoacoustic (PA) technique was used to assess the size and N:C ratio of cultured cancer cells in three dimensions (3D). The diameters of the cells and their stained nuclei were obtained by fitting the power spectrum of backscattered US pulses and emitted PA waves, respectively, to well-established theoretical models. For comparison, an imaging flow cytometer (IFC) was also used to determine the two-dimensional cell and nucleus sizes from large cell populations using brightfield and fluorescence images, respectively. An N:C ratio was calculated for each cell using the quotient of the measured nucleus diameter and the total cell diameter. The mean N:C ratios calculated using the sound-based approach were 0.68, 0.66, and 0.54 for MCF-7, PC-3, and MDA-MB-231 cells, respectively, and were in good agreement with the corresponding values of 0.68, 0.67, and 0.68 obtained using the IFC. The combined US and PA technique, which assesses cellular N:C ratio in 3D, has potential applications in the detection of circulating tumor cells in liquid biopsies.

AGO CLIP Reveals an Activated Network for Acute Regulation of Brain Glutamate Homeostasis in Ischemic Stroke

Post-transcriptional regulation by microRNAs (miRNAs) is essential for complex molecular responses to physiological insult and disease. Although many disease-associated miRNAs are known, their global targets and culminating network effects on pathophysiology remain poorly understood. We applied Argonaute (AGO) crosslinking immunoprecipitation (CLIP) to systematically elucidate altered miRNA-target interactions in brain following ischemia and reperfusion (I/R) injury. Among 1,190 interactions identified, the most prominent was the cumulative loss of target regulation by miR-29 family members. Integration of translational and time-course RNA profiles revealed a dynamic mode of miR-29 target de-regulation, led by acute translational activation and a later increase in RNA levels, allowing rapid proteomic changes to take effect. These functional regulatory events rely on canonical and non-canonical miR-29 binding and engage glutamate reuptake signals, such as glial glutamate transporter (GLT-1), to control local glutamate levels. These results uncover a miRNA target network that acts acutely to maintain brain homeostasis after ischemic stroke.

Plastome phylogenomics of Saussurea (Asteraceae: Cardueae)

BACKGROUND

Saussurea DC. is one of the largest and most morphologically heterogeneous genera in Asteraceae. The relationships within Saussurea have been poorly resolved, probably due an early, rapid radiation. To examine plastome evolution and resolve backbone relationships within Saussurea, we sequenced the complete plastomes of 17 species representing all four subgenera.

RESULTS

All Saussurea plastomes shared the gene content and structure of most Asteraceae plastomes. Molecular evolutionary analysis showed most of the plastid protein-coding genes have been under purifying selection. Phylogenomic analyses of 20 Saussurea plastomes that alternatively included nucleotide or amino acid sequences of all protein-coding genes, vs. the nucleotide sequence of the entire plastome, supported the monophyly of Saussurea and identified three clades within it. Three of the four traditional subgenera were recovered as paraphyletic. Seven plastome regions were identified as containing the highest nucleotide variability.

CONCLUSIONS

Our analyses reveal both the structural conservatism and power of the plastome for resolving relationships in congeneric taxa. It is very likely that differences in topology among data sets is due primarily to differences in numbers of parsimony-informative characters. Our study demonstrates that the current taxonomy of Saussurea is likely based at least partly on convergent morphological character states. Greater taxon sampling will be necessary to explore character evolution and biogeography in the genus. Our results here provide helpful insight into which loci will provide the most phylogenetic signal in Saussurea and Cardueae.

Evolution of Portulacineae Marked by Gene Tree Conflict and Gene Family Expansion Associated with Adaptation to Harsh Environments

Several plant lineages have evolved adaptations that allow survival in extreme and harsh environments including many families within the plant clade Portulacineae (Caryophyllales) such as the Cactaceae, Didiereaceae, and Montiaceae. Here, using newly generated transcriptomic data, we reconstructed the phylogeny of Portulacineae and examined potential correlates between molecular evolution and adaptation to harsh environments. Our phylogenetic results were largely congruent with previous analyses, but we identified several early diverging nodes characterized by extensive gene tree conflict. For particularly contentious nodes, we present detailed information about the phylogenetic signal for alternative relationships. We also analyzed the frequency of gene duplications, confirmed previously identified whole genome duplications (WGD), and proposed a previously unidentified WGD event within the Didiereaceae. We found that the WGD events were typically associated with shifts in climatic niche but did not find a direct association with WGDs and diversification rate shifts. Diversification shifts occurred within the Portulacaceae, Cactaceae, and Anacampserotaceae, and whereas these did not experience WGDs, the Cactaceae experienced extensive gene duplications. We examined gene family expansion and molecular evolutionary patterns with a focus on genes associated with environmental stress responses and found evidence for significant gene family expansion in genes with stress adaptation and clades found in extreme environments. These results provide important directions for further and deeper examination of the potential links between molecular evolutionary patterns and adaptation to harsh environments.

Gross and histopathologic diagnoses from North Atlantic right whale Eubalaena glacialis mortalities between 2003 and 2018

Seventy mortalities of North Atlantic right whales Eubalaena glacialis (NARW) were documented between 2003 and 2018 from Florida, USA, to the Gulf of St. Lawrence, Canada. These included 29 adults, 14 juveniles, 10 calves, and 17 of unknown age class. Females represented 65.5% (19/29) of known-sex adults. Fourteen cases had photos only; 56 carcasses received external examinations, 44 of which were also necropsied. Cause of death was determined in 43 cases, of which 38 (88.4%) were due to anthropogenic trauma: 22 (57.9%) from entanglement, and 16 (42.1%) from vessel strike. Gross and histopathologic lesions associated with entanglement were often severe and included deep lacerations caused by constricting line wraps around the flippers, flukes, and head/mouth; baleen plate mutilation; chronic extensive bone lesions from impinging line, and traumatic scoliosis resulting in compromised mobility in a calf. Chronically entangled whales were often in poor body condition and had increased cyamid burden, reflecting compromised health. Vessel strike blunt force injuries included skull and vertebral fractures, blubber and muscle contusions, and large blood clots. Propeller-induced wounds often caused extensive damage to blubber, muscle, viscera, and bone. Overall prevalence of NARW entanglement mortalities increased from 21% (1970-2002) to 51% during this study period. This demonstrates that despite mitigation efforts, entanglements and vessel strikes continue to inflict profound physical trauma and suffering on individual NARWs. These cumulative mortalities are also unsustainable at the population level, so urgent and aggressive intervention is needed to end anthropogenic mortality in this critically endangered species.

Insights into photoacoustic speckle and applications in tumor characterization

In ultrasound imaging, fully-developed speckle arises from the spatiotemporal superposition of pressure waves backscattered by randomly distributed scatterers. Speckle appearance is affected by the imaging system characteristics (lateral and axial resolution) and the random-like nature of the underlying tissue structure. In this work, we examine speckle formation in acoustic-resolution photoacoustic (PA) imaging using simulations and experiments. Numerical and physical phantoms were constructed to demonstrate that PA speckle carries information related to unresolved absorber structure in a manner similar to ultrasound speckle and unresolved scattering structures. A fractal-based model of the tumor vasculature was used to study PA speckle from unresolved cylindrical vessels. We show that speckle characteristics and the frequency content of PA signals can be used to monitor changes in average vessel size, linked to tumor growth. Experimental validation on murine tumors demonstrates that PA speckle can be utilized to characterize the unresolved vasculature in acoustic-resolution photoacoustic imaging.

Neural microphysiological systems for in vitro modeling of peripheral nervous system disorders

PNS disease pathology is diverse and underappreciated. Peripheral neuropathy may result in sensory, motor or autonomic nerve dysfunction and can be induced by metabolic dysfunction, inflammatory dysfunction, cytotoxic pharmaceuticals, rare hereditary disorders or may be idiopathic. Current preclinical PNS disease research relies heavily on the use of rodent models. In vivo methods are effective but too time-consuming and expensive for high-throughput experimentation. Conventional in vitro methods can be performed with high throughput but lack the biological complexity necessary to directly model in vivo nerve structure and function. In this review, we survey in vitro PNS model systems and propose that 3D-bioengineered microphysiological nerve tissue can improve in vitro–in vivo extrapolation and expand the capabilities of in vitro PNS disease modeling.

Sizing biological cells using a microfluidic acoustic flow cytometer

We describe a new technique that combines ultrasound and microfluidics to rapidly size and count cells in a high-throughput and label-free fashion. Using 3D hydrodynamic flow focusing, cells are streamed single file through an ultrasound beam where ultrasound scattering events from each individual cell are acquired. The ultrasound operates at a center frequency of 375 MHz with a wavelength of 4 μm; when the ultrasound wavelength is similar to the size of a scatterer, the power spectra of the backscattered ultrasound waves have distinct features at specific frequencies that are directly related to the cell size. Our approach determines cell sizes through a comparison of these distinct spectral features with established theoretical models. We perform an analysis of two types of cells: acute myeloid leukemia cells, where 2,390 measurements resulted in a mean size of 10.0 ± 1.7 μm, and HT29 colorectal cancer cells, where 1,955 measurements resulted in a mean size of 15.0 ± 2.3 μm. These results and histogram distributions agree very well with those measured from a Coulter Counter Multisizer 4. Our technique is the first to combine ultrasound and microfluidics to determine the cell size with the potential for multi-parameter cellular characterization using fluorescence, light scattering and quantitative photoacoustic techniques.

PGA: a software package for rapid, accurate, and flexible batch annotation of plastomes

BACKGROUND

Plastome (plastid genome) sequences provide valuable information for understanding the phylogenetic relationships and evolutionary history of plants. Although the rapid development of high-throughput sequencing technology has led to an explosion of plastome sequences, annotation remains a significant bottleneck for plastomes. User-friendly batch annotation of multiple plastomes is an urgent need.

RESULTS

We introduce Plastid Genome Annotator (PGA), a standalone command line tool that can perform rapid, accurate, and flexible batch annotation of newly generated target plastomes based on well-annotated reference plastomes. In contrast to current existing tools, PGA uses reference plastomes as the query and unannotated target plastomes as the subject to locate genes, which we refer to as the reverse query-subject BLAST search approach. PGA accurately identifies gene and intron boundaries as well as intron loss. The program outputs GenBank-formatted files as well as a log file to assist users in verifying annotations. Comparisons against other available plastome annotation tools demonstrated the high annotation accuracy of PGA, with little or no post-annotation verification necessary. Likewise, we demonstrated the flexibility of reference plastomes within PGA by annotating the plastome of Rosa roxburghii using that of Amborella trichopoda as a reference. The program, user manual and example data sets are freely available at https://github.com/quxiaojian/PGA.

CONCLUSIONS

PGA facilitates rapid, accurate, and flexible batch annotation of plastomes across plants. For projects in which multiple plastomes are generated, the time savings for high-quality plastome annotation are especially significant.

How do baleen whales stow their filter? A comparative biomechanical analysis of baleen bending

Bowhead and right whale (balaenid) baleen filtering plates, longer in vertical dimension (≥3-4 m) than the closed mouth, presumably bend during gape closure. This has not been observed in live whales, even with scrutiny of video-recorded feeding sequences. To determine what happens to the baleen during gape closure, we conducted an integrative, multifactorial study including materials testing, functional (flow tank and kinematic) testing and histological examination. We measured baleen bending properties along the dorsoventral length of plates and anteroposterior location within a rack of plates via mechanical (axial bending, composite flexure, compression and tension) tests of hydrated and air-dried tissue samples from balaenid and other whale baleen. Balaenid baleen is remarkably strong yet pliable, with ductile fringes, and low stiffness and high elasticity when wet; it likely bends in the closed mouth when not used for filtration. Calculation of flexural modulus from stress/strain experiments shows that the balaenid baleen is slightly more flexible where it emerges from the gums and at its ventral terminus, but kinematic analysis indicates plates bend evenly along their whole length. Fin and humpback whale baleen has similar material properties but less flexibility, with no dorsoventral variation. The internal horn tubes have greater external and hollow luminal diameter but lower density in the lateral relative to medial baleen of bowhead and fin whales, suggesting a greater capacity for lateral bending. Baleen bending has major consequences not only for feeding morphology and energetics but also for conservation given that entanglement in fishing gear is a leading cause of whale mortality.

Simultaneous ultra-high frequency photoacoustic microscopy and photoacoustic radiometry of zebrafish larvae in vivo

With their optically transparent appearance, zebrafish larvae are readily imaged with optical-resolution photoacoustic (PA) microscopy (OR-PAM). Previous OR-PAM studies have mapped endogenous chromophores (e.g. melanin and hemoglobin) within larvae; however, anatomical features cannot be imaged with OR-PAM alone due to insufficient optical absorption. We have previously reported on the photoacoustic radiometry (PAR) technique, which can be used simultaneously with OR-PAM to generate images dependent upon the optical attenuation properties of a sample. Here we demonstrate application of the duplex PAR/PA technique for label-free imaging of the anatomy and vasculature of zebrafish larvae in vivo at 200 and 400 MHz ultrasound detection frequencies. We then use the technique to assess the effects of anti-angiogenic drugs on the development of the larval vasculature. Our results demonstrate the effectiveness of simultaneous PAR/PA for acquiring anatomical images of optically transparent samples in vivo, and its potential applications in assessing drug efficacy and embryonic development.

Methods for fabrication and evaluation of a 3D microengineered model of myelinated peripheral nerve

OBJECTIVE

The cost and low success rates of the neurological drug development pipeline have diverted the pharmaceutical industry to 'nerve-on-a-chip' systems as preclinical models to streamline drug development. We present a novel micro-engineered 3D hydrogel platform for the culture of myelinated embryonic peripheral neural tissue to serve as an effective in vitro model for electrophysiological and histological analysis that could be adopted for preclinical testing.

APPROACH

Dorsal root ganglions (DRG) from 15 d old embryonic rats were cultured in 3D hydrogel platforms. The interaction between Schwann cells (SC) and neurons during axonal development and regeneration affects the direction of growth and the synthesis of myelin sheaths. Induction of myelination was performed with two approaches: the addition of exogenous SC and promoting migration of endogenous SC.

MAIN RESULTS

Histological analysis of the preparation utilizing exogenous SC showed aligned, highly fasciculated axonal growth with noticeable myelin sheaths around axons. Separately, electrophysiological testing of the preparation utilizing endogenous SC showed increased amplitude of the compound action potential and nerve conduction velocity in the presence of ascorbic acid (AA).

SIGNIFICANCE

This platform has immense potential to be a useful and translatable in vitro testing tool for drug discovery and myelination studies.

Comparison of visible and UVA phototoxicity in neural culture systems micropatterned with digital projection photolithography

Photopolymerization provides a favorable method for hydrogel formation due to its simplicity, convenience, and versatility. However, the light exposure required to initiate photopolymerization is known to have a cytotoxic effect on encapsulated cells. Here, a 3D in vitro model of the nervous system microenvironment, micropatterned through the use of digital projection photolithography using a single hydrogel formulation that cross-links similarly under ultraviolet A (UVA, 315-400 nm) and visible light (400-700 nm) exposure, is presented. This setup allowed for the investigation of neuronal responses to different light wavelengths and exposure times during photoencapsulation, while ruling out effects due to the hydrogel formulation or photoinitiators used. Cellular studies-including neurite viability, DNA fragmentation, and neurite outgrowth for both UVA and visible light irradiation, the most common spectra used in biological photomicropatterning applications-were performed to assess the effect of light source on neuronal cultures. These studies indicated that while cell death occurs after exposure to either spectrum, visible light was less phototoxic than UVA, when using comparable levels of irradiation, and interestingly, glial cells were more susceptible to phototoxicity than neuronal cells. Thus, while utilizing visible light for micropatterning and cell encapsulation for nervous system applications is beneficial, it is helpful to keep the light exposure low to ensure optimal neuronal survival and growth. © 2018 Wiley Periodicals, Inc. J Biomed Mater Res Part A: 107A: 134-144, 2019.

Multi-year patterns in testosterone, cortisol and corticosterone in baleen from adult males of three whale species

Male baleen whales have long been suspected to have annual cycles in testosterone, but due to difficulty in collecting endocrine samples, little direct evidence exists to confirm this hypothesis. Potential influences of stress or adrenal stress hormones (cortisol, corticosterone) on male reproduction have also been difficult to study. Baleen has recently been shown to accumulate steroid hormones during growth, such that a single baleen plate contains a continuous, multi-year retrospective record of the whale's endocrine history. As a preliminary investigation into potential testosterone cyclicity in male whales and influences of stress, we determined patterns in immunoreactive testosterone, two glucocorticoids (cortisol and corticosterone), and stable-isotope (SI) ratios, across the full length of baleen plates from a bowhead whale (Balaena mysticetus), a North Atlantic right whale (Eubalaena glacialis) and a blue whale (Balaenoptera musculus), all adult males. Baleen was subsampled at 2 cm (bowhead, right) or 1 cm (blue) intervals and hormones were extracted from baleen powder with methanol, followed by quantification of all three hormones using enzyme immunoassays validated for baleen extract of these species. Baleen of all three males contained regularly spaced peaks in testosterone content, with number and spacing of testosterone peaks corresponding well to SI data and to species-specific estimates of annual baleen growth rate. Cortisol and corticosterone exhibited some peaks that co-occurred with testosterone peaks, while other glucocorticoid peaks occurred independent of testosterone peaks. The right whale had unusually high glucocorticoids during a period with a known entanglement in fishing gear and a possible disease episode; in the subsequent year, testosterone was unusually low. Further study of baleen testosterone patterns in male whales could help clarify conservation- and management-related questions such as age of sexual maturity, location and season of breeding, and the potential effect of anthropogenic and natural stressors on male testosterone cycles.

Triplex micron-resolution acoustic, photoacoustic, and optical transmission microscopy via photoacoustic radiometry

We present a new sensing technique, termed photoacoustic radiometry (PAR), for mapping the optical attenuation properties of a sample. In PAR, laser pulses attenuated via transmission through the sample impinge on the ultrasound transducer and generate a photoacoustic (PA) signal within it. Spatial variation of the optical attenuation properties of the sample influences the amplitude of the PAR signal, providing image contrast. Performed simultaneously with pulse-echo ultrasound and PA imaging, this triplex imaging technique enables rapid characterization of samples with micrometer-resolution in a single scan. In this work, we demonstrate that the PAR technique can be easily integrated into existing PA microscopy systems, with applications in imaging biological samples and non-destructive evaluation of optically opaque materials such as silicon wafers.

Resting Metabolic Rate and Lung Function in Wild Offshore Common Bottlenose Dolphins, Tursiops truncatus, Near Bermuda

Diving mammals have evolved a suite of physiological adaptations to manage respiratory gases during extended breath-hold dives. To test the hypothesis that offshore bottlenose dolphins have evolved physiological adaptations to improve their ability for extended deep dives and as protection for lung barotrauma, we investigated the lung function and respiratory physiology of four wild common bottlenose dolphins (Tursiops truncatus) near the island of Bermuda. We measured blood hematocrit (Hct, %), resting metabolic rate (RMR, l O₂ ⋅ min^-1), tidal volume (V_T, l), respiratory frequency (f_R, breaths ⋅ min^-1), respiratory flow (l ⋅ min^-1), and dynamic lung compliance (C_L, l ⋅ cmH₂O^-1) in air and in water, and compared measurements with published results from coastal, shallow-diving dolphins. We found that offshore dolphins had greater Hct (56 ± 2%) compared to shallow-diving bottlenose dolphins (range: 30–49%), thus resulting in a greater O₂ storage capacity and longer aerobic diving duration. Contrary to our hypothesis, the specific C_L (sC_L, 0.30 ± 0.12 cmH₂O^-1) was not different between populations. Neither the mass-specific RMR (3.0 ± 1.7 ml O₂ ⋅ min^-1 ⋅ kg^-1) nor V_T (23.0 ± 3.7 ml ⋅ kg^-1) were different from coastal ecotype bottlenose dolphins, both in the wild and under managed care, suggesting that deep-diving dolphins do not have metabolic or respiratory adaptations that differ from the shallow-diving ecotypes. The lack of respiratory adaptations for deep diving further support the recently developed hypothesis that gas management in cetaceans is not entirely passive but governed by alteration in the ventilation-perfusion matching, which allows for selective gas exchange to protect against diving related problems such as decompression sickness.

Plastome characteristics of Cannabaceae

Cannabaceae is an economically important family that includes ten genera and ca. 117 accepted species. To explore the structure and size variation of their plastomes, we sequenced ten plastomes representing all ten genera of Cannabaceae. Each plastome possessed the typical angiosperm quadripartite structure and contained a total of 128 genes. The Inverted Repeat (IR) regions in five plastomes had experienced small expansions (330-983 bp) into the Large Single-Copy (LSC) region. The plastome of Chaetachme aristata has experienced a 942-bp IR contraction and lost rpl22 and rps19 in its IRs. The substitution rates of rps19 and rpl22 decreased after they shifted from the LSC to IR. A 270-bp inversion was detected in the Parasponia rugosa plastome, which might have been mediated by 18-bp inverted repeats. Repeat sequences, simple sequence repeats, and nucleotide substitution rates varied among these plastomes. Molecular markers with more than 13% variable sites and 5% parsimony-informative sites were identified, which may be useful for further phylogenetic analysis and species identification. Our results show strong support for a sister relationship between Gironniera and Lozanell (BS = 100). Celtis, Cannabis-Humulus, Chaetachme-Pteroceltis, and Trema-Parasponia formed a strongly supported clade, and their relationships were well resolved with strong support (BS = 100). The availability of these ten plastomes provides valuable genetic information for accurately identifying species, clarifying taxonomy and reconstructing the intergeneric phylogeny of Cannabaceae.

ZFP36 RNA-binding proteins restrain T cell activation and anti-viral immunity

Dynamic post-transcriptional control of RNA expression by RNA-binding proteins (RBPs) is critical during immune response. ZFP36 RBPs are prominent inflammatory regulators linked to autoimmunity and cancer, but functions in adaptive immunity are less clear. We used HITS-CLIP to define ZFP36 targets in mouse T cells, revealing unanticipated actions in regulating T-cell activation, proliferation, and effector functions. Transcriptome and ribosome profiling showed that ZFP36 represses mRNA target abundance and translation, notably through novel AU-rich sites in coding sequence. Functional studies revealed that ZFP36 regulates early T-cell activation kinetics cell autonomously, by attenuating activation marker expression, limiting T cell expansion, and promoting apoptosis. Strikingly, loss of ZFP36 in vivo accelerated T cell responses to acute viral infection and enhanced anti-viral immunity. These findings uncover a critical role for ZFP36 RBPs in restraining T cell expansion and effector functions, and suggest ZFP36 inhibition as a strategy to enhance immune-based therapies.

The immune system must quickly respond to anything that may cause disease – from cancerous cells to viruses. For instance, a type of white blood cell called a T cell patrols the body, looking for potential threats. If a T cell identifies such a threat, it “activates” and undergoes various changes so that it can help to eliminate the problem.

One way that T cells change is by switching on different genes to make specific proteins. The information in the genes is first used as a template to produce a molecule called a messenger RNA (mRNA), which is then translated to build proteins. So-called RNA-binding proteins help control events before, during and after the translation stage in the process. Previous studies have shown that one particular RNA-binding protein, called ZFP36, controls the translation of proteins that are important for how the immune system recognizes the body’s own tissue and deals with cancer cells. However, it was less clear if it also helped T cells to activate and defeat viruses.

Now, using cutting-edge technology, Moore et al. have identified thousands of new mRNAs controlled by ZFP36 in mice, many of which did indeed make proteins that help T cells activate and spread throughout the body. Further experiments showed that mice that lack ZFP36 in the T cells were much quicker at responding to viruses than other mice. This suggests that ZFP36 actually restrains T cells and slows down the body’s immune system.

Knowing more about how T cells work could lead to new treatments for diseases; it may, for example, allow scientists to engineer T cells to better attack cancer cells, However, other studies have shown that mice without ZFP36 often go on to develop autoimmune diseases, which result from the immune system attacking healthy cells by mistake. As such, it seems that there is a fine line between improving the body’s immune system and increasing the risk of autoimmune diseases, and that RNA-binding proteins play an important role in managing this delicate balance.

Phylogeography of Parasyncalathium souliei (Asteraceae) and Its Potential Application in Delimiting Phylogeoregions in the Qinghai-Tibet Plateau (QTP)-Hengduan Mountains (HDM) Hotspot

Biogeographic regionalization can help to better understand diversity in biogeography, conservation, and macroecology. Historical regionalization schemes typically focus on species distributions, often rarely considering the rich context that phylogeographic information can provide. We investigated whether phylogeographic data could help to delineate floristic regions in the Qinghai-Tibet Plateau (QTP)-Hengduan Mountains (HDM) region by analyzing phylogeographic structure in the herb Parasyncalathium souliei (Asteraceae). We sequenced the plastid psbA-trnH and trnL-rpl32 spacer regions for 417 individuals in 36 populations across the geographic range of the species. To estimate the phylogeographic history of this species, a series of population genetic, phylogenetic, molecular dating, and haplotype network analyses were conducted, as were tested for historical demographic expansions. Using occurrence data, species distribution modeling was used to estimate geographic distributions at three time points: the present, the Mid-Holocene and the Last Glacial Maximum. Significant phylogeographic structure was evident (NST > GST ; P < 0.05) among the 37 haplotypes detected. Four major haplogroups were identified based on phylogenetic analyses. Private haplotypes were restricted to geographically distinct regions that generally corresponded to previously identified biogeographic subregions within the QTP-HDM region. Our results imply Pliocene-Pleistocene diversification of P. souliei and suggest that the species may have been geographically widespread early in its history. This study may provide valuable evidence for phylogeographic regionalization using chloroplast genetic data in a common, widespread endemic species from the QTP-HDM.

Complete plastome sequencing from Toona (Meliaceae) and phylogenomic analyses within Sapindales

PREMISE OF THE STUDY

Toona (Meliaceae, Sapindales) is a small genus of five species of trees native from southern and eastern Asia to New Guinea and Australia. Complete plastomes were sequenced for three Toona species to provide a basis for future plastome genetic studies in threatened species of Toona. In addition, plastome structural evolution and phylogenetic relationships across Sapindales were explored with a larger data set of 29 Sapindales plastomes (including members of six out of nine families).

METHODS

The plastomes were determined using the Illumina sequencing platform; the phylogenetic analyses were conducted using maximum likelihood by RAxML.

RESULTS

The lengths of three Toona plastomes range from 159,185 to 158,196 bp. A total of 113 unique genes were found in each plastome. Across Sapindales, plastome gene structure and content were largely conserved, with the exception of the contraction of the inverted repeat region to exclude ycf1 in some species of Rutaceae and Sapindaceae, and the movement of trnI-GAU and trnA-UGC to a position outside the inverted repeat region in some Rutaceae species.

DISCUSSION

The three Toona plastomes possess the typical structure of angiosperm plastomes. Phylogenomic analysis of Sapindales recovered a mostly strongly supported phylogeny of Sapindales, including most of the backbone relationships, with some improvements compared to previous targeted-gene analyses.