The Pentameric Ligand-Gated Ion Channel Family: A New Member of the Voltage Gated Ion Channel Superfamily?

In this report we present seven lines of bioinformatic evidence supporting the conclusion that the Pentameric Ligand-gated Ion Channel (pLIC) Family is a member of the Voltage-gated Ion Channel (VIC) Superfamily. In our approach, we used the Transporter Classification Database (TCDB) as a reference and applied a series of bioinformatic methods to search for similarities between the pLIC family and members of the VIC superfamily. These include: (1) sequence similarity, (2) compatibility of topology and hydropathy profiles, (3) shared domains, (4) conserved motifs, (5) similarity of Hidden Markov Model profiles between families, (6) common 3D structural folds, and (7) clustering analysis of all families. Furthermore, sequence and structural comparisons as well as the identification of a 3-TMS repeat unit in the VIC superfamily suggests that the sixth transmembrane segment evolved into a re-entrant loop. This evidence suggests that the voltage-sensor domain and the channel domain have a common origin. The classification of the pLIC family within the VIC superfamily sheds light onto the topological origins of this family and its evolution, which will facilitate experimental verification and further research into this superfamily by the scientific community.

Activin E is a transforming growth factor ß ligand that signals specifically through activin receptor-like kinase 7.

Activins are one of the three distinct subclasses within the greater Transforming growth factor ß (TGFß) superfamily. First discovered for their critical roles in reproductive biology, activins have since been shown to alter cellular differentiation and proliferation. At present, members of the activin subclass include activin A (ActA), ActB, ActC, ActE, and the more distant members myostatin and GDF11. While the biological roles and signaling mechanisms of most activins class members have been well-studied, the signaling potential of ActE has remained largely unknown. Here, we characterized the signaling capacity of homodimeric ActE. Molecular modeling of the ligand:receptor complexes showed that ActC and ActE shared high similarity in both the type I and type II receptor binding epitopes. ActE signaled specifically through ALK7, utilized the canonical activin type II receptors, ActRIIA and ActRIIB, and was resistant to the extracellular antagonists follistatin and WFIKKN. In mature murine adipocytes, ActE invoked a SMAD2/3 response via ALK7, like ActC. Collectively, our results establish ActE as a specific signaling ligand which activates the type I receptor, ALK7.

Role of fetal hemoglobin in the development and progression of retinopathy of prematurity in preterm infants.

Purpose: The objective of this study was to find the association between fetal hemoglobin (HbF) concentration and retinopathy of prematurity (ROP) in preterm infants. Methods: In this observational, prospective, longitudinal study, a total of 410 preterm infants with <36 gestational weeks and <2.5 kg birth weight, who were attending ROP clinic in a tertiary care hospital of central India for 1 year duration were included. Dilated fundus examination was done as per ROP screening guidelines, and ROP was staged as per international classification for retinopathy of prematurity (ICROP) classification, 2021. HbF (%) was measured with high-performance liquid chromatography, and data was analyzed statistically. The relationship between HbF (%) and ROP was evaluated. Those infants who had ROP were further divided into treatment-requiring and non-treatment-requiring groups and HbF was compared in these groups at the first visit and after 1-month follow-up period. The outcome of ROP was studied with HbF levels. Results: A total of 410 preterm infants were included, out of which 110 infants had ROP (26.8%). Infants with ROP had significantly lower percentage of HbF with gestational age groups and birth weight groups, compared to infants without ROP. Higher percentage of HbF was associated with a lower prevalence of ROP. Higher concentration of HbF was found in the ROP infants who regressed spontaneously without treatment and less concentration was found in those who progressed to a severe disease and those who required treatment. The predictive ability of HbF (%) was 0.976 for ROP. Conclusion: Low fraction of HbF was found to be significantly associated with the development and progression of ROP.

Activin E is a TGFß ligand that signals specifically through activin receptor-like kinase 7.

Activins are one of the three distinct subclasses within the greater Transforming Growth Factor ß (TGFß) superfamily. First discovered for their critical roles in reproductive biology, activins have since been shown to alter cellular differentiation and proliferation. At present, members of the activin subclass include activin A (ActA), ActB, ActC, ActE, and the more distant members myostatin and GDF11. While the biological roles and signaling mechanisms of most activins class members have been well-studied, the signaling potential of ActE has remained largely unknown. Here, we characterized the signaling capacity of homodimeric ActE. Molecular modeling of the ligand:receptor complexes showed that ActC and ActE shared high similarity in both the type I and type II receptor binding epitopes. ActE signaled specifically through ALK7, utilized the canonical activin type II receptors, ActRIIA and ActRIIB, and was resistant to the extracellular antagonists follistatin and WFIKKN. In mature murine adipocytes, ActE invoked a SMAD2/3 response via ALK7, similar to ActC. Collectively, our results establish ActE as an ALK7 ligand, thereby providing a link between genetic and in vivo studies of ActE as a regulator of adipose tissue.

Fetal hemoglobin, blood transfusion, and retinopathy of prematurity in preterm infants: An observational, prospective study.

Purpose: The objective of this study was to identify the association between fetal hemoglobin (HbF) concentration, blood transfusion, and retinopathy of prematurity (ROP) in preterm infants. Methods: This was an observational, prospective study. A total of 410 preterm infants born with <36 weeks gestational age and <2.0 kg birth weight in a tertiary care center of central India for a period of 1 year were included in this study. Clinical data were obtained from case notes. HbF of infants was measured in the blood sample using high-performance liquid chromatography at the first visit and after 1 month follow-up and was analyzed statistically. Dilated fundus examination was done as per ROP screening guidelines, and ROP was classified as per the International Classification of Retinopathy of Prematurity (ICROP), 2021. The study subjects were divided into two groups based on the status of ROP. The relationship among HbF, blood transfusion, and ROP was evaluated in both the groups. The relationship between other clinical characteristics and various neonatal risk factors was also studied between the groups. Results: A total of 410 preterm infants were included in this study, of which 110 infants had ROP (26.8%). Blood transfusion was found to be significantly associated with the development of ROP. Higher fraction of HbF (%) was associated with a lower prevalence of ROP. HbF was also inversely related with the severity of ROP. Conclusion: Replacing HbF by adult hemoglobin during blood transfusion may promote the development of ROP. Conversely, maintaining a higher percentage of HbF may be a protective factor against ROP.

Bilateral Optic Neuropathy in Association with Diffuse Cutaneous Systemic Sclerosis with Interstitial Lung Disease.

PURPOSE: To report a rare case of bilateral optic neuropathy in a patient with diffuse cutaneous systemic sclerosis with interstitial lung disease. METHOD: Retrospective case report. RESULT: A middle-aged female, who was a known case of systemic sclerosis with interstitial lung disease, was presented with sudden painless bilateral loss of vision for a month. The fundoscopy findings were suggestive of bilateral optic atrophy. Anti-topoisomerase I was found in the serum. Serum B12 and folate levels were reduced. HRCT Chest was suggestive of interstitial lung disease. MRI brain was normal and MRI orbit showed kinking of the left optic nerve. The findings were suggestive of diffuse cutaneous systemic sclerosis with interstitial lung disease and bilateral optic neuropathy. CONCLUSION: This is a rare case of bilateral optic neuropathy in a patient with diffuse cutaneous systemic sclerosis and interstitial lung disease with profound vision loss, in the absence of renal or cardiac involvement.

Rare loss of function variants in the hepatokine gene INHBE protect from abdominal obesity.

Identifying genetic variants associated with lower waist-to-hip ratio can reveal new therapeutic targets for abdominal obesity. We use exome sequences from 362,679 individuals to identify genes associated with waist-to-hip ratio adjusted for BMI (WHRadjBMI), a surrogate for abdominal fat that is causally linked to type 2 diabetes and coronary heart disease. Predicted loss of function (pLOF) variants in INHBE associate with lower WHRadjBMI and this association replicates in data from AMP-T2D-GENES. INHBE encodes a secreted protein, the hepatokine activin E. In vitro characterization of the most common INHBE pLOF variant in our study, indicates an in-frame deletion resulting in a 90% reduction in secreted protein levels. We detect associations with lower WHRadjBMI for variants in ACVR1C, encoding an activin receptor, further highlighting the involvement of activins in regulating fat distribution. These findings highlight activin E as a potential therapeutic target for abdominal obesity, a phenotype linked to cardiometabolic disease.

Anterior patterning genes induced by Zic1 are sensitive to retinoic acid and its metabolite, 4-oxo-RA.

BACKGROUND: Development of paired sensory organs is a highly complex and coordinated process. These organs arise from ectodermal thickenings in the cephalic region known as cranial placodes. We have previously shown that Zic1 is a critical regulator for the formation of the pre-placodal region (PPR), the common territory for the development of all cranial placodes in Xenopus laevis. RESULTS: In this study, we have analyzed a number of Zic1 targets for their expression during PPR patterning, as well as their regulation by retinoic acid (RA) and one of its major metabolites, 4-oxo-RA. Our findings show that anteriorly Zic1 regulates several transcription factors, Crx, Fezf2, Nkx3-1, and Xanf1 as well as a serine/threonine/tyrosine kinase, Pkdcc.2. These factors are all expressed in the vicinity of the PPR and as such are candidate regulators of placode formation downstream of Zic1. In addition to their differential regulation by RA, we find that 4-oxo-RA is also capable of modulating the expression of these genes, as well as a broad array of RA-regulated genes. CONCLUSION: Our data highlight the complexity of retinoid-mediated regulation required for Zic1-activated anterior structure specification in Xenopus, and the potential physiological role of 4-oxo-RA in cranial placode development.

Comparative population genomic analyses of transporters within the Asgard archaeal superphylum.

Upon discovery of the first archaeal species in the 1970s, life has been subdivided into three domains: Eukarya, Archaea, and Bacteria. However, the organization of the three-domain tree of life has been challenged following the discovery of archaeal lineages such as the TACK and Asgard superphyla. The Asgard Superphylum has emerged as the closest archaeal ancestor to eukaryotes, potentially improving our understanding of the evolution of life forms. We characterized the transportomes and their substrates within four metagenome-assembled genomes (MAGs), that is, Odin-, Thor-, Heimdall- and Loki-archaeota as well as the fully sequenced genome of Candidatus Prometheoarchaeum syntrophicum strain MK-D1 that belongs to the Loki phylum. Using the Transporter Classification Database (TCDB) as reference, candidate transporters encoded within the proteomes were identified based on sequence similarity, alignment coverage, compatibility of hydropathy profiles, TMS topologies and shared domains. Identified transport systems were compared within the Asgard superphylum as well as within dissimilar eukaryotic, archaeal and bacterial organisms. From these analyses, we infer that Asgard organisms rely mostly on the transport of substrates driven by the proton motive force (pmf), the proton electrochemical gradient which then can be used for ATP production and to drive the activities of secondary carriers. The results indicate that Asgard archaea depend heavily on the uptake of organic molecules such as lipid precursors, amino acids and their derivatives, and sugars and their derivatives. Overall, the majority of the transporters identified are more similar to prokaryotic transporters than eukaryotic systems although several instances of the reverse were documented. Taken together, the results support the previous suggestions that the Asgard superphylum includes organisms that are largely mixotrophic and anaerobic but more clearly define their metabolic potential while providing evidence regarding their relatedness to eukaryotes.

Retinoic acid production, regulation and containment through Zic1, Pitx2c and Cyp26c1 control cranial placode specification.

All paired sensory organs arise from a common precursor domain called the pre-placodal region (PPR). In Xenopus, Zic1 non-cell autonomously regulates PPR formation by activating retinoic acid (RA) production. Here, we have identified two Zic1 targets, the RA catabolizing enzyme Cyp26c1 and the transcription factor Pitx2c, expressed in the vicinity of the PPR as being crucially required for maintaining low RA levels in a spatially restricted, PPR-adjacent domain. Morpholino- or CRISPR/Cas9-mediated Cyp26c1 knockdown abrogated PPR gene expression, yielding defective cranial placodes. Direct measurement of RA levels revealed that this is mediated by a mechanism involving excess RA accumulation. Furthermore, we show that pitx2c is activated by RA and required for Cyp26c1 expression in a domain-specific manner through induction of FGF8. We propose that Zic1 anteriorly establishes a program of RA containment and regulation through activation of Cyp26c1 and Pitx2c that cooperates to promote PPR specification in a spatially restricted domain.

Effects of clothianidin-treated seed on the arthropod community in a mid-Atlantic no-till corn agroecosystem.

BACKGROUND: Nearly all corn seed in the US is coated with neonicotinoid insecticides to protect against soil and foliar arthropod pests. Exposure in the soil and the systemic activity in the plant can pose non-target risks. We assessed the community-level effects of clothianidin-treated seed on the diversity and abundance of arthropod communities in a no-till corn agroecosystem over a single growing season. RESULTS: Epigeal and foliage-dwelling communities were disturbed by the clothianidin seed treatment, with significant negative and positive changes in taxa abundances. Clothianidin reduced the abundance of minute pirate bugs by 66.2%, lady beetles by 44.7%, ants by 43.4%, ground beetle adults and larvae by 31.7%, and rove beetles by 44.1% during the early corn growth stages. Herbivores, particularly thrips, were more negatively affected by clothianidin than other trophic groups. In contrast, some groups, such as collembolans and leafhoppers, exhibited significantly higher abundances in the seed treated plots. CONCLUSION: Clothianidin primarily influenced arthropod communities during the 4 weeks following planting, with disruptions to major natural enemy taxa, but communities showed trends toward recovery at the later corn stages. While the insecticide suppressed multiple herbivores, none were economically damaging to corn; thus, the pest suppression benefits of clothianidin observed in this study did not justify the non-target impacts. © 2018 Society of Chemical Industry.

Bowman's layer transplantation: evidence to date.

Surgical management of keratoconus (KC) has undergone a paradigm shift in the last two decades and component corneal transplantation technique of deep anterior lamellar keratoplasty has established itself as a modality of choice for management of advanced cases of KC. Every now and then, new minimalist modalities are being innovated for the management of KC. On the same lines, a new technique, Bowman's layer transplantation, for surgical management of moderate to advanced KC has been reported in recent years. The procedure has shown to be beneficial in reducing ectasia in advanced KC with minimal intraoperative and postoperative complications. In this review, we intend to describe available information and literature with reference to this new surgical technique - Bowman's layer transplantation.

Generating retinoic acid gradients by local degradation during craniofacial development: One cell's cue is another cell's poison.

Retinoic acid (RA) is a vital morphogen for early patterning and organogenesis in the developing embryo. RA is a diffusible, lipophilic molecule that signals via nuclear RA receptor heterodimeric units that regulate gene expression by interacting with RA response elements in promoters of a significant number of genes. For precise RA signaling, a robust gradient of the morphogen is required. The developing embryo contains regions that produce RA, and specific intracellular concentrations of RA are created through local degradation mediated by Cyp26 enzymes. In order to elucidate the mechanisms by which RA executes precise developmental programs, the kinetics of RA metabolism must be clearly understood. Recent advances in techniques for endogenous RA detection and quantification have paved the way for mechanistic studies to shed light on downstream gene expression regulation coordinated by RA. It is increasingly coming to light that RA signaling operates not only at precise concentrations but also employs mechanisms of degradation and feedback inhibition to self-regulate its levels. A global gradient of RA throughout the embryo is often found concurrently with several local gradients, created by juxtaposed domains of RA synthesis and degradation. The existence of such local gradients has been found especially critical for the proper development of craniofacial structures that arise from the neural crest and the cranial placode populations. In this review, we summarize the current understanding of how local gradients of RA are established in the embryo and their impact on craniofacial development.

Epidemiology, clinical profile and factors, predicting final visual outcome of pediatric ocular trauma in a tertiary eye care center of Central India.

PURPOSE: Ocular trauma constitutes an important cause of preventable visual morbidity worldwide. This study was done to study the incidence, sociodemographic pattern, and clinical profile of ocular trauma in pediatric age group. Also to evaluate the factors influencing final visual outcome in these patients. METHODS: This was a prospective interventional study concerning ocular trauma in pediatric patients up to 16 years of age of either sex. Various variables having an impact on final visual outcome were studied, and results were analyzed using statistical indices - relative risk, Chi-square test, P value, and linear regression analysis. RESULTS: A total of 220 cases of trauma were evaluated with the mean age being 8.74 ± 3.93 years, males were predominantly affected and open globe injuries outnumbered blunt injuries. Penetrating injuries accounted for 67.79% cases of open globe injury, rupture being the least (2.54%). Stepwise multiple linear regression analysis executed, showed the best predictors in the descending order for final visual outcome were presenting visual acuity, size of corneal tear, type of injury, zone of injury, time period between injury and treatment with a variance of 35.9%, 6.3%, 5.3%, 3.7%, and 2.7%, respectively. All above variables were also found to be statistically significant (P < 0.05) on Chi-square test. CONCLUSION: We report the first study on the epidemiology and clinical outcomes of pediatric ocular trauma in central India. Poor initial Visual Acuity and posterior segment involvement adversely affect the visual outcome. Early medical treatment and globe-salvaging repair should be done in all eyes suffering from trauma.

Modeling human craniofacial disorders in Xenopus.

PURPOSE OF REVIEW: Craniofacial disorders are among the most common human birth defects and present an enormous health care and social burden. The development of animal models has been instrumental to investigate fundamental questions in craniofacial biology and this knowledge is critical to understand the etiology and pathogenesis of these disorders. RECENT FINDINGS: The vast majority of craniofacial disorders arise from abnormal development of the neural crest, a multipotent and migratory cell population. Therefore, defining the pathogenesis of these conditions starts with a deep understanding of the mechanisms that preside over neural crest formation and its role in craniofacial development. SUMMARY: This review discusses several studies using Xenopus embryos to model human craniofacial conditions, and emphasizes the strength of this system to inform important biological processes as they relate to human craniofacial development and disease.

The Selenocysteine-Specific Elongation Factor Contains Unique Sequences That Are Required for Both Nuclear Export and Selenocysteine Incorporation.

Selenocysteine (Sec) is a critical residue in at least 25 human proteins that are essential for antioxidant defense and redox signaling in cells. Sec is inserted into proteins cotranslationally by the recoding of an in-frame UGA termination codon to a Sec codon. In eukaryotes, this recoding event requires several specialized factors, including a dedicated, Sec-specific elongation factor called eEFSec, which binds Sec-tRNASec with high specificity and delivers it to the ribosome for selenoprotein production. Unlike most translation factors, including the canonical elongation factor eEF1A, eEFSec readily localizes to the nucleus of mammalian cells and shuttles between the cytoplasmic and nuclear compartments. The functional significance of eEFSec's nuclear localization has remained unclear. In this study, we have examined the subcellular localization of eEFSec in the context of altered Sec incorporation to demonstrate that reduced selenoprotein production does not correlate with changes in the nuclear localization of eEFSec. In addition, we identify several novel sequences of the protein that are essential for localization as well as Sec insertion activity, and show that eEFSec utilizes CRM1-mediated nuclear export pathway. Our findings argue for two distinct pools of eEFSec in the cell, where the cytoplasmic pool participates in Sec incorporation and the nuclear pool may be involved in an as yet unknown function.

Management of advanced corneal ectasias.

Corneal ectasias include a group of disorders characterised by progressive thinning, bulging and distortion of the cornea. Keratoconus is the most common disease in this group. Other manifestations include pellucid marginal degeneration, Terrien's marginal degeneration, keratoglobus and ectasias following surgery. Advanced ectasias usually present with loss of vision due to high irregular astigmatism. Management of these disorders is difficult due to the peripheral location of ectasia and associated severe corneal thinning. Newer contact lenses such as scleral lenses are helpful in a selected group of patients. A majority of these cases requires surgical intervention. This review provides an update on the current treatment modalities available for management of advanced corneal ectasias.

An x-ray absorption spectroscopy study of Ni-Mn-Ga shape memory alloys.

The austenite to martensite phase transition in Ni-Mn-Ga ferromagnetic shape memory alloys was studied by extended x-ray absorption fine structure (EXAFS) and x-ray absorption near-edge structure (XANES) spectroscopy. The spectra at all the three elements', namely, Mn, Ga and Ni, K-edges in several Ni-Mn-Ga samples (with both Ni and Mn excess) were analyzed at room temperature and low temperatures. The EXAFS analysis suggested a displacement of Mn and Ga atoms in opposite direction with respect to the Ni atoms when the compound transforms from the austenite phase to the martensite phase. The first coordination distances around the Mn and Ga atoms remained undisturbed on transition, while the second and subsequent shells showed dramatic changes indicating the presence of a modulated structure. The Mn rich compounds showed the presence of antisite disorder of Mn and Ga. The XANES results showed remarkable changes in the unoccupied partial density of states corresponding to Mn and Ni, while the electronic structure of Ga remained unperturbed across the martensite transition. The post-edge features in the Mn K-edge XANES spectra changed from a double peak like structure to a flat peak like structure upon phase transition. The study establishes strong correlation between the crystal structure and the unoccupied electronic structure in these shape memory alloys.

The molecular biology of selenocysteine.

Selenium is an essential trace element that is incorporated into 25 human proteins as the amino acid selenocysteine (Sec). The incorporation of this amino acid turns out to be a fascinating problem in molecular biology because Sec is encoded by a stop codon, UGA. Layered on top of the canonical translation elongation machinery is a set of factors that exist solely to incorporate this important amino acid. The mechanism by which this process occurs, put into the context of selenoprotein biology, is the focus of this review.

A streamlined sub-cloning procedure to transfer shRNA from a pSM2 vector to a pGIPZ lentiviral vector.

RNA interference (RNAi) is a widely used molecular biology technique to investigate the importance of specific genes in molecular pathways. Since mammalian cells are equipped with endogenous RNAi processing machinery, it has become common practice to transfect constructs that encode for short hairpin RNAs that are then cleaved to form the active RNAi sequences that bind to target mRNAs. Given the profit potential of this research approach, companies have developed retroviral libraries of shRNA constructs targeting the majority of the human genes. Recent technologic advances have allowed the rapid improvement of the vectors carrying the shRNA constructs while the silencing sequences remain the same. Therefore, sub-cloning of shRNA sequences from more obsolete vectors to newer vectors is a straightforward way to take advantage of newer delivery technologies. We describe here a streamlined procedure to transfer shRNA sequences from the pSM2 retroviral vector to a newer pGIPZ vector that is more stable, contains a GFP cassette and allows the preparation of high titer viral particles for transduction of cells and in vivo use. We demonstrate that our protocol provides a cost-effective and fast method to successfully sub-clone shRNA from a pSM2 retroviral vector to a pGIPZ lentiviral vector making it a useful tool for the investigators that have purchased pSM2 vectors in the past and wish now to upgrade their constructs by inserting them in more versatile vectors.