Effect of traditional roughage-based or limit-fed, high-energy diets on growth performance and digestion in newly received growing cattle and subsequent implications on feedlot growth performance and carcass characteristics.

The objective was to determine the effects of ad libitum-fed roughage-based diets or limit-fed high-energy diets on growth performance, behavior, health, and digestion in newly received growing cattle and subsequent implications on feedlot growth performance and carcass characteristics. In experiment 1, 409 crossbred heifers (initial body weight [BW] = 279 ±â€…24 kg) in 32 pens were used in a randomized block design. Heifers were fed one of two dietary treatments: a total mixed ration with 0.99 Mcal net energy for gain (NEg)/kg dry matter (DM) fed ad libitum (0.99AL) or 1.32 Mcal NEg/kg DM limit-fed at 85% of intake of heifers fed 0.99AL (1.32LF85%). Both diets contained 40% DM as a branded wet corn gluten feed. In experiment 2, 370 crossbred heifers (initial BW = 225 ±â€…20 kg) were used in a randomized block design and were fed a diet formulated to contain 0.99 Mcal of NEg/kg DM for ad libitum intake or a diet formulated to contain 1.32 Mcal of NEg/kg DM and fed at 2.2% of BW daily (DM basis; 1.32LF2.2). For experiments 1 and 2, treatment integrity was maintained through the finishing phase where cattle were fed a common diet. Cattle were sorted by BW into heavy and light groups prior to finishing, with light cattle fed longer than heavy cattle to reach similar harvest BW. In experiment 3, eight ruminally cannulated heifers (average BW = 305 ±â€…23 kg) were used in a 2-period cross-over design and fed treatments from experiment 1 to assess digestibility and ruminal fermentation characteristics. Gain:feed was 47% and 35% greater (P < 0.01) in experiments 1 and 2, respectively, for limit-fed heifers compared with 0.99AL heifers. Rumination time was greater (P < 0.01) for 0.99AL compared with limit-fed treatments in experiments 1 and 2. Activity was greater (P < 0.01) for 1.32LF2.2 than for 0.99AL in experiment 2. In experiment 1, more (P = 0.03) carcasses from light-sort heifers than carcasses from heavy-sort heifers had livers with large, active abscesses. In experiment 2, finishing phase morbidity was greater (P < 0.01) for 1.32LF2.2 than for 0.99AL. Light-sort groups had fewer (P < 0.01) edible livers than heavy-sort groups, suggesting that greater number of days on feed may increase the risk of liver abscess prevalence and condemnation. In experiment 3, apparent total-tract DM and organic matter digestibilities were greater (P < 0.01) for 1.32LF85% than for 0.99AL. Overall, dietary treatments during the growing phase had little carryover effect on feedlot growth performance, carcass characteristics, or liver abscesses prevalence at harvest.

Velocity changes in femoral vessel ultrasound with Doppler in Porcine hemorrhagic shock.

Objective: Physician-directed point-of-care ultrasound (PoCUS) is routinely used to identify the etiology of shock and guide therapy in the ICU. We performed a preclinical study to determine what changes are manifested in the femoral vessels during hemorrhagic shock on Duplex imaging and to generate a femoral vessel sonographic profile over the time course of shock. Design & setting: A preclinical study in swine was performed using a convenience sample of animals that were being used in a Trauma Surgery training lab. The animals developed progressive unregulated hemorrhage during the lab. Subjects: Six anesthetized swine underwent Duplex studies of the femoral vessels prior to any hemorrhage and at two time points after the start of hemorrhage. Interventions: N/A. Measurements: Femoral vessel imaging was performed using a portable ultrasound (Sonosite and Clarius). Main results: Femoral arterial peak systolic velocity decreased in all animals with hemorrhage, from a mean (SD) of 77 (27) cm/s pre-hemorrhage to 42 (17) and 32 (16) cm/s at the two post-hemorrhage time points. There were also changes to the arterial waveform morphology. Mean venous velocities also decreased with hemorrhage (20, 11, 7 cm/s). Animals with severe hemorrhage had a cessation of venous flow during positive pressure ventilation. Conclusion: In this preclinical study, both femoral peak systolic velocity and venous velocity decreased with hemorrhage. Femoral vessels represent an easily accessible target for non-invasive hemodynamic monitoring. Changes in femoral vessel Duplex waveforms and velocities should be studied both in a larger sample of animals with controlled hemorrhage and in human trauma patients to determine whether changes appear in early hemorrhage, before the onset of clinically evident hemorrhagic shock.

Paternal imprinting in Marchantia polymorpha.

We are becoming aware of a growing number of organisms that do not express genetic information equally from both parents as a result of an epigenetic phenomenon called genomic imprinting. Recently, it was shown that the entire paternal genome is repressed during the diploid phase of the life cycle of the liverwort Marchantia polymorpha. The deposition of the repressive epigenetic mark H3K27me3 on the male pronucleus is responsible for the imprinted state, which is reset by the end of meiosis. Here, we put these recent reports in perspective of other forms of imprinting and discuss the potential mechanisms of imprinting in bryophytes and the causes of its evolution.

Focused Assessment with Sonography for Trauma (FAST) Exam: Image Acquisition.

Over the past twenty years, the Focused Assessment with Sonography for Trauma (FAST) exam has transformed the care of patients presenting with a combination of trauma (blunt or penetrating) and hypotension. In these hemodynamically unstable trauma patients, the FAST exam permits rapid and noninvasive screening for free pericardial or peritoneal fluid, the latter of which implicates intra-abdominal injury as a likely contributor to the hypotension and justifies emergent abdominal surgical exploration. Further, the abdominal portion of the FAST exam can also be used outside of the trauma setting to screen for free peritoneal fluid in patients who become hemodynamically unstable in any context, including after procedures that may inadvertently injure abdominal organs. These "non-trauma" situations of hemodynamic instability are often triaged by providers from specialties other than emergency medicine or trauma surgery who are not familiar with the FAST exam. Therefore, there is a need to promulgate knowledge about the FAST exam to all clinicians caring for critically ill patients. Toward this end, this article describes FAST exam image acquisition: patient positioning, transducer selection, image optimization, and exam limitations. Since the free fluid is likely to be found in specific anatomic locations that are unique for each canonical FAST exam view, this work centers on the unique image acquisition considerations for each window: subcostal, right upper quadrant, left upper quadrant, and pelvis.

The Polycomb repressive complex 2 deposits H3K27me3 and represses transposable elements in a broad range of eukaryotes.

The mobility of transposable elements (TEs) contributes to evolution of genomes. Their uncontrolled activity causes genomic instability; therefore, expression of TEs is silenced by host genomes. TEs are marked with DNA and H3K9 methylation, which are associated with silencing in flowering plants, animals, and fungi. However, in distantly related groups of eukaryotes, TEs are marked by H3K27me3 deposited by the Polycomb repressive complex 2 (PRC2), an epigenetic mark associated with gene silencing in flowering plants and animals. The direct silencing of TEs by PRC2 has so far only been shown in one species of ciliates. To test if PRC2 silences TEs in a broader range of eukaryotes, we generated mutants with reduced PRC2 activity and analyzed the role of PRC2 in extant species along the lineage of Archaeplastida and in the diatom P. tricornutum. In this diatom and the red alga C. merolae, a greater proportion of TEs than genes were repressed by PRC2, whereas a greater proportion of genes than TEs were repressed by PRC2 in bryophytes. In flowering plants, TEs contained potential cis-elements recognized by transcription factors and associated with neighbor genes as transcriptional units repressed by PRC2. Thus, silencing of TEs by PRC2 is observed not only in Archaeplastida but also in diatoms and ciliates, suggesting that PRC2 deposited H3K27me3 to silence TEs in the last common ancestor of eukaryotes. We hypothesize that during the evolution of Archaeplastida, TE fragments marked with H3K27me3 were selected to shape transcriptional regulation, controlling networks of genes regulated by PRC2.

Evaluation of commercially available point-of-care ultrasound for automated optic nerve sheath measurement.

BACKGROUND: Measurement of the optic nerve sheath diameter (ONSD) via ultrasonography has been proposed as a non-invasive metric of intracranial pressure that may be employed during in-field patient triage. However, first responders are not typically trained to conduct sonographic exams and/or do not have access to an expensive ultrasound device. Therefore, for successful deployment of ONSD measurement in-field, we believe that first responders must have access to low-cost, portable ultrasound and be assisted by artificial intelligence (AI) systems that can automatically interpret the optic nerve sheath ultrasound scan. We examine the suitability of five commercially available, low-cost, portable ultrasound devices that can be combined with future artificial intelligence algorithms to reduce the training required for and cost of in-field optic nerve sheath diameter measurement. This paper is focused on the quality of the images generated by these low-cost probes. We report results of a clinician preference survey and compare with a lab analysis of three quantitative image quality metrics across devices. We also examine the suitability of the devices in a hypothetical far-forward deployment using operators unskilled in ultrasound, with the assumption of a future onboard AI video interpreter. RESULTS: We find statistically significant differences in clinician ranking of the devices in the following categories: "Image Quality", "Ease of Acquisition", "Software", and "Overall ONSD". We show differences in signal-to-noise ratio, generalized contrast-to-noise ratio, point-spread function across the devices. These differences in image quality result in a statistically significant difference in manual ONSD measurement. Finally, we show that sufficiently wide transducers can capture the optic nerve sheath during blind (no visible B-mode) scans performed by operators unskilled in sonography. CONCLUSIONS: Ultrasound of the optic nerve sheath has the potential to be a convenient, non-invasive, point-of-injury or triage measure for elevated intracranial pressure in cases of traumatic brain injury. When transducer width is sufficient, briefly trained operators may obtain video sequences of the optic nerve sheath without guidance. This data suggest that unskilled operators are able to achieve the images needed for AI interpretation. However, we also show that image quality differences between ultrasound probes may influence manual ONSD measurements.

Optic Nerve Sheath Point of Care Ultrasound: Image Acquisition.

The goal of this protocol is to develop a standardized method for acquiring images of the optic nerve sheath and measuring the optic nerve sheath diameter (ONSD). Diagnostic ultrasound of the ONSD to detect intracranial hypertension has traditionally faced many problems because of methodologic discrepancies. Due to inconsistencies in the measuring techniques, the potential for ONSD to become a non-invasive bedside monitoring tool for ICP has been hampered. However, establishing a transparent, consistent methodology for measuring the ONSD would support its use as a valid and reliable method of identifying intracranial hypertension. This is important as it has both high sensitivity and specificity in acute care settings. This narrative review describes ONSD POCUS image acquisition, including patient positioning, transducer selection, probe placement, the acquisition sequence, and image optimization. Further, visual aids are provided to assist in real-time during image acquisition. This method should be considered for patients for whom there are concerns regarding intracranial hypertension but who do not have an intracranial monitor in place.

Point-of-Care Lung Ultrasound in Adults: Image Acquisition.

Consultative ultrasound performed by radiologists has traditionally not been used for imaging the lungs, as the lungs' air-filled nature normally prevents direct visualization of the lung parenchyma. When showing the lung parenchyma, ultrasound typically generates a number of non-anatomic artifacts. However, over the past several decades, these artifacts have been studied by diagnostic point-of-care ultrasound (POCUS) practitioners, who have identified findings that have value in narrowing the differential diagnoses of cardiopulmonary dysfunction. For instance, in patients presenting with dyspnea, lung POCUS is superior to chest radiography (CXR) for the diagnosis of pneumothorax, pulmonary edema, lung consolidations, and pleural effusions. Despite its known diagnostic value, the utilization of lung POCUS in clinical medicine remains variable, in part because training in this modality across hospitals remains inconsistent. To address this educational gap, this narrative review describes lung POCUS image acquisition in adults, including patient positioning, transducer selection, probe placement, acquisition sequence, and image optimization.

Detection of pneumothorax on ultrasound using artificial intelligence.

BACKGROUND: Ultrasound (US) for the detection of pneumothorax shows excellent sensitivity in the hands of skilled providers. Artificial intelligence may facilitate the movement of US for pneumothorax into the prehospital setting. The large amount of training data required for conventional neural network methodologies has limited their use in US so far. METHODS: A limited training database was supplied by Defense Advanced Research Projects Agency of 30 patients, 15 cases with pneumothorax and 15 cases without. There were two US videos per patient, of which we were allowed to choose one to train on, so that a limited set of 30 videos were used. Images were annotated for ribs and pleural interface. The software performed anatomic reconstruction to identify the region of interest bounding the pleura. Three neural networks were created to analyze images on a pixel-by-pixel fashion with direct voting determining the outcome. Independent verification and validation was performed on a data set gathered by the Department of Defense. RESULTS: Anatomic reconstruction with the identification of ribs and pleura was able to be accomplished on all images. On independent verification and validation against the Department of Defense testing data, our program concurred with the SME 80% of the time and achieved a 86% sensitivity (18/21) for pneumothorax and a 75% specificity for the absence of pneumothorax (18/24). Some of the mistakes by our artificial intelligence can be explained by chest wall motion, hepatization of the underlying lung, or being equivocal cases. CONCLUSION: Using learning with limited labeling techniques, pneumothorax was identified on US with an accuracy of 80%. Several potential improvements are controlling for chest wall motion and the use of longer videos. LEVEL OF EVIDENCE: Diagnostic Tests; Level III.

Image Acquisition Method for the Sonographic Assessment of the Inferior Vena Cava.

Over the past several decades, clinicians have incorporated several applications of diagnostic point-of-care ultrasound (POCUS) into medical decision-making. Among the applications of POCUS, imaging the inferior vena cava (IVC) is practiced by a wide variety of specialties, such as nephrology, emergency medicine, internal medicine, critical care, anesthesiology, pulmonology, and cardiology. Although each specialty uses IVC data in slightly different ways, most medical specialties, at minimum, attempt to use IVC data to make predictions about intravascular volume status. While the relationship between IVC sonographic data and intravascular volume status is complex and highly context-dependent, all clinicians should collect the sonographic data in standardized ways to ensure repeatability. This paper describes standardized IVC image acquisition including patient positioning, transducer selection, probe placement, image optimization, and the pitfalls and limitations of IVC sonographic imaging. This paper also describes the commonly performed anterior IVC long-axis view and three other views of the IVC that can each provide helpful diagnostic information when the anterior long-axis view is difficult to obtain or interpret.

Polycomb-mediated repression of paternal chromosomes maintains haploid dosage in diploid embryos of Marchantia.

Complex mechanisms regulate gene dosage throughout eukaryotic life cycles. Mechanisms controlling gene dosage have been extensively studied in animals, however it is unknown how generalizable these mechanisms are to diverse eukaryotes. Here, we use the haploid plant Marchantia polymorpha to assess gene dosage control in its short-lived diploid embryo. We show that throughout embryogenesis, paternal chromosomes are repressed resulting in functional haploidy. The paternal genome is targeted for genomic imprinting by the Polycomb mark H3K27me3 starting at fertilization, rendering the maternal genome in control of embryogenesis. Maintaining haploid gene dosage by this new form of imprinting is essential for embryonic development. Our findings illustrate how haploid-dominant species can regulate gene dosage through paternal chromosome inactivation and initiates the exploration of the link between life cycle history and gene dosage in a broader range of organisms.

The reproductive cells of organisms that reproduce sexually ­ the egg and the sperm ­ each contain one copy of the organism's genome. An embryo forms upon fertilization of an egg by a sperm cell. This embryo contains two copies of the genome, one from each parent. Under most circumstances, it does not matter which parent a gene copy came from: both gene copies are expressed. However, in some species genes coming from only one of the parents are switched on. This unusual mode of gene expression is called genomic imprinting. The best-known example of this occurs in female mammals, which repress the genes on the paternal X chromosome. Genomic imprinting also exists in flowering plants. Both mammals and flowering plants evolved tissues that channel nutrients from the mother to the embryo during development; the placenta and the endosperm, respectively. Genomic imprinting had, until now, only been described in these two types of organisms. It was unknown whether imprinting also happens in other organisms, and specifically those in which embryos develop inside the mother but without the help of a placenta or endosperm. Here Montgomery et al. addressed this question by studying the liverwort, Marchantia polymorpha, a moss-like plant. Initial experiments showed that cells in the liverwort embryo mostly expressed the genes coming from the egg, and not the sperm. All the genetic material coming from the sperm had a molecular marker or tag called H3K27me3. This mark, which also appears on the paternal X chromosome in female mammals, switches off the genes it tags. M. polymorpha embryos thus suppress gene expression from all of the genetic material from the father, relying only on maternal genetic material for development. When Montgomery et al. deleted the maternal genes necessary for making the H3K27me3 mark, the paternal genes switched on, and this led to the death of the embryos. The survival of M. polymorpha embryos therefore depended on keeping only one set of genes active. Taken together these experiments indicate that genomic imprinting evolved about 480 million years ago, about 320 million years earlier than previously thought, in organisms for which embryo development depended only on one parent. This means there are likely many more organisms that control gene expression in this way, opening up opportunities for further research. Understanding imprinting in more detail will also shed light on how sexual reproduction evolved.

Effects of feeding corn containing an alpha-amylase gene on the performance and digestibility of growing cattle.

Two growth performance studies and two digestibility trials were conducted to evaluate the effects of feeding Enogen Feed Corn silage and corn grain to growing cattle. In Exp. 1, there were a total of four diets offered for ad libitum intake. The four diets consisted of two varieties of corn (Enogen Feed Corn [EFC] vs. yellow #2 corn [CON]) with two different methods of corn processing (dry-rolled [DR] vs. whole-shelled [WS]) and were formulated to provide 1.13 Mcal NEg/kg dry matter (DM); corn grain was 28.6% of diet DM. Average daily gain (ADG) and ending body weight tended to be greater for calves fed EFC than for those fed CON (P < 0.10). Gain:feed (G:F) was better for calves fed EFC (P < 0.01), improving by 5.5% over calves fed CON. In Exp. 2, a digestibility trial was conducted using seven cannulated Holstein steers fed the same diets from Exp. 1. Ruminal pH was not affected by corn variety (P > 0.82). Liquid passage rate was greater for CON-fed calves and associated with lower digestibility. Total tract DM and organic matter (OM) digestibilities were greater for EFC-fed calves (P < 0.04). In Exp. 3, there were four diets offered for ad libitum intake. Dietary factors were arranged as a 2 × 2 factorial and consisted of two hybrids of corn silage (EFC silage [EFC-S] vs. control silage [CON-S]) and two varieties of corn grain (EFC grain [EFC-G] vs. control [CON-G]; both were dry-rolled). Diets were formulated to provide 1.11 Mcal NEg/kg DM; corn grain was 38.5% of diet DM, and corn silage was 40% of diet DM. ADG was 6.0% greater (P < 0.01) and G:F was numerically (P < 0.14) 3.3% greater for calves fed EFC-S than for those fed CON-S, but substituting EFC-G for CON-G did not affect ADG or G:F. In Exp. 4, a digestibility trial was conducted using eight cannulated beef steers fed the same diets as Exp. 3. Liquid passage rate (P > 0.20), ruminal pH (P > 0.23), and ruminal total volatile fatty acid concentrations (P > 0.27) were unaffected by treatment. Total tract digestibilities of DM and OM were numerically greater by 2.5% and 2.2%, respectively, for calves fed the EFC-S compared with those fed CON-S. Feeding a corn hybrid containing alpha-amylase enzyme improved G:F of growing calves. Feeding EFC can benefit the beef industry by allowing less processing of grain without sacrificing performance.

A Portable Negative Pressure Isolation System as a Solution to Minimize Exposure of Health Care Providers to Infectious Pathogens.

The COVID-19 pandemic has resulted in the exposure of many surgeons and healthcare providers (HCPs) to disease given high patient loads and limited availability of negative pressure rooms. For these reasons we pursued the development of a portable patient isolation system (COVIAGE™ by iSolace, Inc.) that can be used to contain patients with respiratory illness and minimize the exposure of HCPs. COVIAGE™ is comprised of a reusable aluminum frame, a disposable thermoplastic polyurethane tent and a HEPA filtration/ventilation system (HVAC) utilizing two inline filters. The efficacy of filtration was tested by comparing particulate concentration inside and outside of the device by an independent third party. Additionally, physician, nursing, and respiratory tasks were performed initially on simulated patients and then on intubated patients in the ICU. The system attained a verified filtration efficiency greater than 99.999% for an average 0.3-µm size particulates. Simulation testing revealed that most common physician, nursing, and respiratory tasks could be completed in the device, including endotracheal intubation. Emergency removal of the device can be accomplished in 8.8 ± 2.8 seconds. The reusable aluminum frame allows for simple attachment to the bed, and adaptability to different types and sizes of beds/stretchers. An emergency use authorization was granted by the FDA. The device created results in a portable negative pressure isolation system that can be placed over the patient's bed to contain aerosols during high aerosol generating procedures, transportation of patients or for total patient care in environments where negative pressure rooms are not available.

Identification of the sex-determining factor in the liverwort Marchantia polymorpha reveals unique evolution of sex chromosomes in a haploid system.

Sex determination is a central process for sexual reproduction and is often regulated by a sex determinant encoded on a sex chromosome. Rules that govern the evolution of sex chromosomes via specialization and degeneration following the evolution of a sex determinant have been well studied in diploid organisms. However, distinct predictions apply to sex chromosomes in organisms where sex is determined in the haploid phase of the life cycle: both sex chromosomes, female U and male V, are expected to maintain their gene functions, even though both are non-recombining. This is in contrast to the X-Y (or Z-W) asymmetry and Y (W) chromosome degeneration in XY (ZW) systems of diploids. Here, we provide evidence that sex chromosomes diverged early during the evolution of haploid liverworts and identify the sex determinant on the Marchantia polymorpha U chromosome. This gene, Feminizer, encodes a member of the plant-specific BASIC PENTACYSTEINE transcription factor family. It triggers female differentiation via regulation of the autosomal sex-determining locus of FEMALE GAMETOPHYTE MYB and SUPPRESSOR OF FEMINIZATION. Phylogenetic analyses of Feminizer and other sex chromosome genes indicate dimorphic sex chromosomes had already been established 430 mya in the ancestral liverwort. Feminizer also plays a role in reproductive induction that is shared with its gametolog on the V chromosome, suggesting an ancestral function, distinct from sex determination, was retained by the gametologs. This implies ancestral functions can be preserved after the acquisition of a sex determination mechanism during the evolution of a dominant haploid sex chromosome system.

An Unusual Timing of Amoxicillin-Induced IgA Vasculitis in an Elderly Patient.

Immunoglobulin A vasculitis is a small vessel vasculitis which is usually common in the pediatric group. It is rare in adult population but more severe than in children. Proposed triggers include infections, malignancy and medications. For most part, the association is made when immunoglobulin A vasculitis develops within two weeks after starting the implicated medication. A 66-year-old male who was treated with amoxicillin/clavulanate for presumed right fourth toe infection but returned to the emergency department 48 hours later with palpable purpura of lower limbs, arthralgia with swollen hands and colicky abdominal pain with nausea. Abdominal computed tomography (CT) scan showed mildly dilated small bowel. Skin biopsies showed leukocytoclastic vasculitis with IgA deposit on immunofluorescence. The patient was treated with a short course of steroid and the rash was significantly reduced during subsequent follow-up. Although amoxicillin/clavulanate is widely prescribed, clinicians need to be aware of this risk and immediately stop it if signs of drug-induced vasculitis develop.

The evolution of imprinting in plants: beyond the seed.

Genomic imprinting results in the biased expression of alleles depending on if the allele was inherited from the mother or the father. Despite the prevalence of sexual reproduction across eukaryotes, imprinting is only found in placental mammals, flowering plants, and some insects, suggesting independent evolutionary origins. Numerous hypotheses have been proposed to explain the selective pressures that favour the innovation of imprinted gene expression and each differs in their experimental support and predictions. Due to the lack of investigation of imprinting in land plants, other than angiosperms with triploid endosperm, we do not know whether imprinting occurs in species lacking endosperm and with embryos developing on maternal plants. Here, we discuss the potential for uncovering additional examples of imprinting in land plants and how these observations may provide additional support for one or more existing imprinting hypotheses.

The chromatin remodeler DDM1 prevents transposon mobility through deposition of histone variant H2A.W.

Mobile transposable elements (TEs) not only participate in genome evolution but also threaten genome integrity. In healthy cells, TEs that encode all of the components that are necessary for their mobility are specifically silenced, yet the precise mechanism remains unknown. Here, we characterize the mechanism used by a conserved class of chromatin remodelers that prevent TE mobility. In the Arabidopsis chromatin remodeler DECREASE IN DNA METHYLATION 1 (DDM1), we identify two conserved binding domains for the histone variant H2A.W, which marks plant heterochromatin. DDM1 is necessary and sufficient for the deposition of H2A.W onto potentially mobile TEs, yet does not act on TE fragments or host protein-coding genes. DDM1-mediated H2A.W deposition changes the properties of chromatin, resulting in the silencing of TEs and, therefore, prevents their mobility. This distinct mechanism provides insights into the interplay between TEs and their host in the contexts of evolution and disease, and potentiates innovative strategies for targeted gene silencing.

A Synthetic Approach to Reconstruct the Evolutionary and Functional Innovations of the Plant Histone Variant H2A.W.

Diversification of histone variants is marked by the acquisition of distinct motifs and functional properties through convergent evolution.1-4 H2A variants are distinguished by specific C-terminal motifs and tend to be segregated within defined domains of the genome.5,6 Whether evolution of these motifs pre-dated the evolution of segregation mechanisms or vice versa has remained unclear. A suitable model to address this question is the variant H2A.W, which evolved in plants through acquisition of a KSPK motif7 and is tightly associated with heterochromatin.4 We used fission yeast, where chromatin is naturally devoid of H2A.W, to study the impact of engineered chimeras combining yeast H2A with the KSPK motif. Biochemical assays showed that the KSPK motif conferred nucleosomes with specific properties. Despite uniform incorporation of the engineered H2A chimeras in the yeast genome, the KSPK motif specifically affected heterochromatin composition and function. We conclude that the KSPK motif promotes chromatin properties in yeast that are comparable to the properties and function of H2A.W in plant heterochromatin. We propose that the selection of functional motifs confer histone variants with properties that impact primarily a specific chromatin state. The association between a new histone variant and a preferred chromatin state can thus provide a setting for the evolution of mechanisms that segregate the new variant to this state, thereby enhancing the impact of the selected properties of the variant on genome activity.

Marchantia TCP transcription factor activity correlates with three-dimensional chromatin structure.

Information in the genome is not only encoded within sequence or epigenetic modifications, but is also found in how it folds in three-dimensional space. The formation of self-interacting genomic regions, named topologically associated domains (TADs), is known as a key feature of genome organization beyond the nucleosomal level. However, our understanding of the formation and function of TADs in plants is extremely limited. Here we show that the genome of Marchantia polymorpha, a member of a basal land plant lineage, exhibits TADs with epigenetic features similar to those of higher plants. By analysing various epigenetic marks across Marchantia TADs, we find that these regions generally represent interstitial heterochromatin and their borders are enriched with Marchantia transcription factor TCP1. We also identify a type of TAD that we name 'TCP1-rich TAD', in which genomic regions are highly accessible and are densely bound by TCP1 proteins. Transcription of TCP1 target genes differs on the basis gene location, and those in TCP1-rich TADs clearly show a lower expression level. In tcp1 mutant lines, neither TCP1-bound TAD borders nor TCP1-rich TADs display drastically altered chromatin organization patterns, suggesting that, in Marchantia, TCP1 is dispensable for TAD formation. However, we find that in tcp1 mutants, genes residing in TCP1-rich TADs have a greater extent of expression fold change as opposed to genes that do not belong to these TADs. Our results suggest that, besides standing as spatial chromatin-packing modules, plant TADs function as nuclear microcompartments associated with transcription factor activities.

The evolution and functional divergence of the histone H2B family in plants.

Chromatin regulation of eukaryotic genomes depends on the formation of nucleosome complexes between histone proteins and DNA. Histone variants, which are diversified by sequence or expression pattern, can profoundly alter chromatin properties. While variants in histone H2A and H3 families are well characterized, the extent of diversification of histone H2B proteins is less understood. Here, we report a systematic analysis of the histone H2B family in plants, which have undergone substantial divergence during the evolution of each major group in the plant kingdom. By characterising Arabidopsis H2Bs, we substantiate this diversification and reveal potential functional specialization that parallels the phylogenetic structure of emergent clades in eudicots. In addition, we identify a new class of highly divergent H2B variants, H2B.S, that specifically accumulate during chromatin compaction of dry seed embryos in multiple species of flowering plants. Our findings thus identify unsuspected diverse properties among histone H2B proteins in plants that has manifested into potentially novel groups of histone variants.