Genetic analysis of the Replication Protein A large subunit family in Arabidopsis reveals unique and overlapping roles in DNA repair, meiosis and DNA replication

Replication Protein A (RPA) is a heterotrimeric protein complex that binds single-stranded DNA. In plants, multiple genes encode the three RPA subunits (RPA1, RPA2 and RPA3), including five RPA1-like genes in Arabidopsis. Phylogenetic analysis suggests two distinct groups composed of RPA1A, RPA1C, RPA1E (ACE group) and RPA1B, RPA1D (BD group). ACE-group members are transcriptionally induced by ionizing radiation, while BD-group members show higher basal transcription and are not induced by ionizing radiation. Analysis of rpa1 T-DNA insertion mutants demonstrates that although each mutant line is likely null, all mutant lines are viable and display normal vegetative growth. The rpa1c and rpa1e single mutants however display hypersensitivity to ionizing radiation, and combination of rpa1c and rpa1e results in additive hypersensitivity to a variety of DNA damaging agents. Combination of the partially sterile rpa1a with rpa1c results in complete sterility, incomplete synapsis and meiotic chromosome fragmentation, suggesting an early role for RPA1C in promoting homologous recombination. Combination of either rpa1c and/or rpa1e with atr revealed additive hypersensitivity phenotypes consistent with each functioning in unique repair pathways. In contrast, rpa1b rpa1d double mutant plants display slow growth and developmental defects under non-damaging conditions. We show these defects in the rpa1b rpa1d mutant are likely the result of defective DNA replication leading to reduction in cell division

Novel opsin gene variation in large-bodied, diurnal lemurs

Some primate populations include both trichromatic and dichromatic (red-green colour blind) individuals due to allelic variation at the X-linked opsin locus. This polymorphic trichromacy is well described in day-active New World monkeys. Less is known about colour vision in Malagasy lemurs, but, unlike New World monkeys, only some day-active lemurs are polymorphic, while others are dichromatic. The evolutionary pressures underlying these differences in lemurs are unknown, but aspects of species ecology, including variation in activity pattern, are hypothesized to play a role. Limited data on X-linked opsin variation in lemurs make such hypotheses difficult to evaluate. We provide the first detailed examination of X-linked opsin variation across a lemur clade (Indriidae). We sequenced the X-linked opsin in the most strictly diurnal and largest extant lemur, Indri indri, and nine species of smaller, generally diurnal indriids (Propithecus). Although nocturnal Avahi (sister taxon to Propithecus) lacks a polymorphism, at least eight species of diurnal indriids have two or more X-linked opsin alleles. Four rainforest-living taxa-I. indri and the three largest Propithecus species-have alleles not previously documented in lemurs. Moreover, we identified at least three opsin alleles in Indri with peak spectral sensitivities similar to some New World monkeys

Tracking smell loss to identify healthcare workers with SARS-CoV-2 infection

Introduction Healthcare workers (HCW) treating COVID-19 patients are at high risk for infection and may also spread infection through their contact with vulnerable patients. Smell loss has been associated with SARS-CoV-2 infection, but it is unknown whether monitoring for smell loss can be used to identify asymptomatic infection among high risk individuals. In this study we sought to determine if tracking smell sensitivity and loss using an at-home assessment could identify SARS-CoV-2 infection in HCW. Methods and findings We performed a prospective cohort study tracking 473 HCW across three months to determine if smell loss could predict SARS-CoV-2 infection in this high-risk group. HCW subjects completed a longitudinal, behavioral at-home assessment of olfaction with household items, as well as detailed symptom surveys that included a parosmia screening questionnaire, and real-time quantitative polymerase chain reaction testing to identify SARS-CoV-2 infection. Our main measures were the prevalence of smell loss in SARS-CoV-2-positive HCW versus SARS-CoV- 2-negative HCW, and timing of smell loss relative to SARS-CoV-2 test positivity. SARS-CoV-2 was identified in 17 (3.6%) of 473 HCW. HCW with SARS-CoV-2 infection were more likely to report smell loss than SARS-CoV-2-negative HCW on both the at-home assessment and the screening questionnaire (9/17, 53% vs 105/456, 23%, P < .01). 6/9 (67%) of SARS-CoV-2-positive HCW reporting smell loss reported smell loss prior to having a positive SARS-CoV-2 test, and smell loss was reported a median of two days before testing positive. Neurological symptoms were reported more frequently among SARS-CoV-2-positive HCW who reported smell loss compared to those without smell loss (9/9, 100% vs 3/8, 38%, P < .01). Conclusions In this prospective study of HCW, self-reported changes in smell using two different measures were predictive of SARS-CoV-2 infection. Smell loss frequently preceded a positive test and was associated with neurological symptoms

Strategies to Mitigate and Treat Orthopaedic Device-Associated Infections

Orthopaedic device implants play a crucial role in restoring functionality to patients suffering from debilitating musculoskeletal diseases or to those who have experienced traumatic injury. However, the surgical implantation of these devices carries a risk of infection, which represents a significant burden for patients and healthcare providers. This review delineates the pathogenesis of orthopaedic implant infections and the challenges that arise due to biofilm formation and the implications for treatment. It focuses on research advancements in the development of next-generation orthopaedic medical devices to mitigate against implant-related infections. Key considerations impacting the development of devices, which must often perform multiple biological and mechanical roles, are delineated. We review technologies designed to exert spatial and temporal control over antimicrobial presentation and the use of antimicrobial surfaces with intrinsic antibacterial activity. A range of measures to control bio-interfacial interactions including approaches that modify implant surface chemistry or topography to reduce the capacity of bacteria to colonise the surface, form biofilms and cause infections at the device interface and surrounding tissues are also reviewed

Data from: Genome sequence and population declines in the critically endangered greater bamboo lemur (Prolemur simus) and implications for conservation

Background: The greater bamboo lemur (Prolemur simus) is a member of the Family Lemuridae that is unique in their dependency on bamboo as a primary food source. This Critically Endangered species lives in small forest patches in eastern Madagascar, occupying a fraction of its historical range. Here we sequence the genome of the greater bamboo lemur for the first time, and provide genome resources for future studies of this species that can be applied across its distribution. Results: Following whole genome sequencing of five individuals we identified over 152,000 polymorphic single nucleotide variants (SNVs), and evaluated geographic structuring across nearly 19k SNVs. We characterized a stronger signal associated with a north-south divide than across elevations for our limited samples. We also evaluated the demographic history of this species, and infer a dramatic population crash. This species had the largest effective population size (estimated between ~900,000 to one million individuals) between approximately 60,000-90,000 years before present (ybp), during a time in which global climate change affected terrestrial mammals worldwide. We also note the single sample from the northern portion of the extant range had the largest effective population size around 35,000 ybp. Conclusions: From our whole genome sequencing we recovered an average genomic heterozygosity of 0.0037%, comparable to other lemurs. Our demographic history reconstructions recovered a probable climate-related decline (60-90,000 ybp), followed by a second population decrease following human colonization, which has reduced the species to a census size of approximately 1,000 individuals. The historical distribution was likely a vast portion of Madagascar, minimally estimated at 44,259 km2, while the contemporary distribution is only ~1,700 km2. The decline in effective population size of 89-99.9% corresponded to a vast range retraction. Conservation management of this species is crucial to retain genetic diversity across the remaining isolated populations

Data from: Genome sequence and population declines in the critically endangered greater bamboo lemur (Prolemur simus) and implications for conservation

Background: The greater bamboo lemur (Prolemur simus) is a member of the Family Lemuridae that is unique in their dependency on bamboo as a primary food source. This Critically Endangered species lives in small forest patches in eastern Madagascar, occupying a fraction of its historical range. Here we sequence the genome of the greater bamboo lemur for the first time, and provide genome resources for future studies of this species that can be applied across its distribution. Results: Following whole genome sequencing of five individuals we identified over 152,000 polymorphic single nucleotide variants (SNVs), and evaluated geographic structuring across nearly 19k SNVs. We characterized a stronger signal associated with a north-south divide than across elevations for our limited samples. We also evaluated the demographic history of this species, and infer a dramatic population crash. This species had the largest effective population size (estimated between ~900,000 to one million individuals) between approximately 60,000-90,000 years before present (ybp), during a time in which global climate change affected terrestrial mammals worldwide. We also note the single sample from the northern portion of the extant range had the largest effective population size around 35,000 ybp. Conclusions: From our whole genome sequencing we recovered an average genomic heterozygosity of 0.0037%, comparable to other lemurs. Our demographic history reconstructions recovered a probable climate-related decline (60-90,000 ybp), followed by a second population decrease following human colonization, which has reduced the species to a census size of approximately 1,000 individuals. The historical distribution was likely a vast portion of Madagascar, minimally estimated at 44,259 km2, while the contemporary distribution is only ~1,700 km2. The decline in effective population size of 89-99.9% corresponded to a vast range retraction. Conservation management of this species is crucial to retain genetic diversity across the remaining isolated populations

The mesocolon

Background: Colonic mobilization requires separation of mesocolon from underlying fascia. Despite the surgical importance of planes formed by these structures, no study has formally characterized their microscopic features. The aim of this study was to determine the histological and electron microscopic appearance of mesocolon, fascia, and retroperitoneum, prior to and after colonic mobilization. Methods: In 24 cadavers, samples were taken from right, transverse, descending, and sigmoid mesocolon. In 12 cadavers, specimens were stained with hematoxylin and eosin (3 sections) or Masson trichrome (3 sections). In the second 12 cadavers, lymphatic channels were identified by staining immunohistochemically for podoplanin. The ascending mesocolon was assessed with scanning electron microscopy. The above process was first conducted with the mesocolon in situ. The mesocolon was then surgically mobilized, and the process was repeated on remaining structures. Results: The microscopic structure of mesocolon and associated fascia was consistent from ileocecal to mesorectal level. A surface mesothelium and underlying connective tissue were evident throughout. Fibrous septae separated adipocyte lobules. Where apposed to retroperitoneum, 2 mesothelial layers separated mesocolon and underlying retroperitoneum. A connective tissue layer occurred between these (ie, Toldt\u27s fascia). Lymphatic channels were evident both in mesocolic connective tissue and Toldt\u27s fascia. After surgical separation of mesocolon and fascia both remained contiguous, the fascia remained in situ and the retroperitoneum undisturbed. Conclusions: The findings demonstrate that the contiguous mesocolon and retroperitoneum are separated by mesothelial and connective tissue layers. These properties generate the surgical planes (ie, meso-and retrofascial planes) exploited in colonic and mesocolic mobilization

The mesocolon

Background: Colonic mobilization requires separation of mesocolon from underlying fascia. Despite the surgical importance of planes formed by these structures, no study has formally characterized their microscopic features. The aim of this study was to determine the histological and electron microscopic appearance of mesocolon, fascia, and retroperitoneum, prior to and after colonic mobilization. Methods: In 24 cadavers, samples were taken from right, transverse, descending, and sigmoid mesocolon. In 12 cadavers, specimens were stained with hematoxylin and eosin (3 sections) or Masson trichrome (3 sections). In the second 12 cadavers, lymphatic channels were identified by staining immunohistochemically for podoplanin. The ascending mesocolon was assessed with scanning electron microscopy. The above process was first conducted with the mesocolon in situ. The mesocolon was then surgically mobilized, and the process was repeated on remaining structures. Results: The microscopic structure of mesocolon and associated fascia was consistent from ileocecal to mesorectal level. A surface mesothelium and underlying connective tissue were evident throughout. Fibrous septae separated adipocyte lobules. Where apposed to retroperitoneum, 2 mesothelial layers separated mesocolon and underlying retroperitoneum. A connective tissue layer occurred between these (ie, Toldt's fascia). Lymphatic channels were evident both in mesocolic connective tissue and Toldt's fascia. After surgical separation of mesocolon and fascia both remained contiguous, the fascia remained in situ and the retroperitoneum undisturbed. Conclusions: The findings demonstrate that the contiguous mesocolon and retroperitoneum are separated by mesothelial and connective tissue layers. These properties generate the surgical planes (ie, meso-and retrofascial planes) exploited in colonic and mesocolic mobilization

Additional file 2: of Genome sequence and population declines in the critically endangered greater bamboo lemur (Prolemur simus) and implications for conservation

Supplementary Materials detailing permits, genome assembly, MAKER annotation, Demographic history reconstruction- Propithecus and Microcebus, VCF Filtration. (DOCX 31 kb

Additional file 4: of Genome sequence and population declines in the critically endangered greater bamboo lemur (Prolemur simus) and implications for conservation

BUSCO v2.0beta assessments of genome completeness for the five different genome assemblies, using the ‘mammal’ set of 4106 genes. (DOCX 46 kb