Fungal coexistence in the skin mycobiome: a study involving Malassezia, Candida, and Rhodotorula.

Evidence of fungal coexistence in humans points towards fungal adaptation to the host environment, like the skin. The human commensal Malassezia has evolved, especially residing in sebum-rich areas of the mammalian body where it can get the necessary nutrition for its survival. This fungus is primarily responsible for skin diseases like Pityriasis versicolor (PV), characterized by hypo or hyperpigmented skin discoloration and erythematous macules. In this manuscript, we report a 19-year-old healthy female who presented with a one-year history of reddish, hypopigmented, asymptomatic lesions over the chest and a raised erythematous lesion over the face. Upon clinical observation, the patient displayed multiple erythematous macules and erythematous papules over the bilateral malar area of the face, along with multiple hypopigmented scaly macules present on the chest and back. Based on the above clinical findings, a diagnosis of PV and Acne vulgaris (AV) was made. Interestingly, the patient was immunocompetent and didn't have any comorbidities. Upon isolation of skin scrapings and post-culturing, we found the existence of three fungal genera in the same region of the patient's body. We further went on to confirm the identity of the particular species and found it to represent Malassezia, Rhodotorula, and Candida. We report how Malassezia, the predominant microbial resident skin fungus, coexists with other fungal members of the skin mycobiome. This study on an applied aspect of microbiology also shows how important it is to identify the fungal organism associated with skin infections so that appropriate therapeutics can be advised to avoid cases of relapse.

BRCA1 interactors, RAD50 and BRIP1, as prognostic markers for triple-negative breast cancer severity.

Introduction: BRIP1 (BRCA1-interacting protein 1) is one of the major interacting partners of BRCA1, which plays an important role in repair by homologous recombination (HR). This gene is mutated in around 4% of cases of breast cancer; however, its mechanism of action is unclear. In this study, we presented the fundamental role of BRCA1 interactors BRIP1 and RAD50 in the development of differential severity in triple-negative breast cancer (TNBC) among various affected individuals. Methods: We have analyzed the expression of DNA repair-related genes in different BC cells using Real-time PCR and western blotting analysis and assessed changes in stemness property and proliferation through Immunophenotyping. We have performed cell cycle analysis to see the defect in checkpoints and also immunofluorescence assay to confirm the accumulation of gamma-H2AX and BRCA1 foci and subsequent incidence. We have performed a severity analysis using TCGA data sets for comparing the expression in MDA-MB-468 MDA-MB-231 and MCF7 cell line. Results: We showed that in some TNBC cell lines such as MDA-MB-231, the functioning of both BRCA1/TP53 is compromised. Furthermore, the sensing of DNA damage is affected. Due to less damage-sensing capability and low availability of BRCA1 at the damage sites, the repair by HR becomes inefficient, leading to more damage. Accumulation of damage sends a signal for over activation of NHEJ repair pathways. Over expressed NHEJ molecules with compromised HR and checkpoint conditions lead to higher proliferation and error-prone repair, which increases the mutation rate and corresponding tumour severity. The in-silico analysis of the TCGA datasets with gene expression in the deceased population showed a significant correlation of BRCA1 expression with overall survival (OS) in TNBCs (0.0272). The association of BRCA1 with OS became stronger with the addition of BRIP1 expression (0.000876**). Conclusion: The severity phenotypes were more in cells having compromised BRCA1-BRIP1 functioning. Since the OS is directly proportional to the extent of severity, the data analysis hints at the role of BRIP1 in controlling the severity of TNBC.

Configurational entropy from a replica approach: A density-functional model.

We study a field-theoretic model for the metastable liquid using a nonlocal free-energy functional with density ρ(x) is the order parameter and three-point correlation effects included in the formulation. We assume fragmentation of the free-energy landscape into distinct basins of local minima and evaluate the partition function for the many-particle system through mapping into a composite system of m identical replicas. Static correlations and configurational entropy S_{c} are calculated in the m=1 limit. The Kauzman packing fraction η_{K} obtained are in agreement with other works.

Localization, Disorder, and Entropy in a Coarse-Grained Model of the Amorphous Solid.

We study the role of disorder in producing the metastable states in which the extent of mass localization is intermediate between that of a liquid and a crystal with long-range order. We estimate the corresponding entropy with the coarse-grained description of a many-particle system used in the classical density functional model. We demonstrate that intermediate localization of the particles results in a change of the entropy from what is obtained from a microscopic approach using for sharply localized vibrational modes following a Debye distribution. An additional contribution is included in the density of vibrational states g(ω) to account for this excess entropy. A corresponding peak in g(ω)/ω2 vs. frequency ω matches the characteristic boson peak seen in amorphous solids. In the present work, we also compare the shear modulus for the inhomogeneous solid having localized density profiles with the corresponding elastic response for the uniform liquid in the limit of high frequencies.

Genetic Susceptibility to Fungal Infections and Links to Human Ancestry.

Over the ages, fungi have associated with different parts of the human body and established symbiotic associations with their host. They are mostly commensal unless there are certain not so well-defined factors that trigger the conversion to a pathogenic state. Some of the factors that induce such transition can be dependent on the fungal species, environment, immunological status of the individual, and most importantly host genetics. In this review, we discuss the different aspects of how host genetics play a role in fungal infection since mutations in several genes make hosts susceptible to such infections. We evaluate how mutations modulate the key recognition between the pathogen associated molecular patterns (PAMP) and the host pattern recognition receptor (PRR) molecules. We discuss the polymorphisms in the genes of the immune system, the way it contributes toward some common fungal infections, and highlight how the immunological status of the host determines fungal recognition and cross-reactivity of some fungal antigens against human proteins that mimic them. We highlight the importance of single nucleotide polymorphisms (SNPs) that are associated with several of the receptor coding genes and discuss how it affects the signaling cascade post-infection, immune evasion, and autoimmune disorders. As part of personalized medicine, we need the application of next-generation techniques as a feasible option to incorporate an individual's susceptibility toward invasive fungal infections based on predisposing factors. Finally, we discuss the importance of studying genomic ancestry and reveal how genetic differences between the human race are linked to variation in fungal disease susceptibility.

The budding yeast protein Chl1p is required for delaying progression through G1/S phase after DNA damage.

BACKGROUND: The budding yeast protein Chl1p is a nuclear protein required for sister-chromatid cohesion, transcriptional silencing, rDNA recombination, ageing and plays an instrumental role in chromatin remodeling. This helicase is known to preserve genome integrity and spindle length in S-phase. Here we show additional roles of Chl1p at G1/S phase of the cell cycle following DNA damage. RESULTS: G1 arrested cells when exposed to DNA damage are more sensitive and show bud emergence with faster kinetics in chl1 mutants compared to wild-type cells. Also, more damage to DNA is observed in chl1 cells. The viability falls synergistically in rad24chl1 cells. The regulation of Chl1p on budding kinetics in G1 phase falls in line with Rad9p/Chk1p and shows a synergistic effect with Rad24p/Rad53p. rad9chl1 and chk1chl1 shows similar bud emergence as the single mutants chl1, rad9 and chk1. Whereas rad24chl1 and rad53chl1 shows faster bud emergence compared to the single mutants rad24, rad53 and chl1. In presence of MMS induced damage, synergistic with Rad24p indicates Chl1p's role as a checkpoint at G1/S acting parallel to damage checkpoint pathway. The faster movement of DNA content through G1/S phase and difference in phosphorylation profile of Rad53p in wild type and chl1 cells confirms the checkpoint defect in chl1 mutant cells. Further, we have also confirmed that the checkpoint defect functions in parallel to the damage checkpoint pathway of Rad24p. CONCLUSION: Chl1p shows Rad53p independent bud emergence and Rad53p dependent checkpoint activity in presence of damage. This confirms its requirement in two different pathways to maintain the G1/S arrest when cells are exposed to damaging agents. The bud emergence kinetics and DNA segregation were similar to wild type when given the same damage in nocodazole treated chl1 cells which establishes the absence of any role of Chl1p at the G2/M phase. The novelty of this paper lies in revealing the versatile role of Chl1p in checkpoints as well as repair towards regulating G1/S transition. Chl1p thus regulates the G1/S phase by affecting the G1 replication checkpoint pathway and shows an additive effect with Rad24p for Rad53p activation when damaging agents perturb the DNA. Apart from checkpoint activation, it also regulates the budding kinetics as a repair gene.

The repair gene BACH1 - a potential oncogene.

BACH1 encodes for a protein that belongs to RecQ DEAH helicase family and interacts with the BRCT repeats of BRCA1. The N-terminus of BACH1 functions in DNA metabolism as DNA-dependent ATPase and helicase. The C-terminus consists of BRCT domain, which interacts with BRCA1 and this interaction is one of the major regulator of BACH1 function. BACH1 plays important roles both in phosphorylated as well as dephosphorylated state and functions in coordination with multiple signaling molecules. The active helicase property of BACH1 is maintained by its dephosphorylated state. Imbalance between these two states enhances the development and progression of the diseased condition. Currently BACH1 is known as a tumor suppressor gene based on the presence of its clinically relevant mutations in different cancers. Through this review we have justified it to be named as an oncogene. In this review, we have explained the mechanism of how BACH1 in collaboration with BRCA1 or independently regulates various pathways like cell cycle progression, DNA replication during both normal and stressed situation, recombination and repair of damaged DNA, chromatin remodeling and epigenetic modifications. Mutation and overexpression of BACH1 are significantly found in different cancer types. This review enlists the molecular players which interact with BACH1 to regulate DNA metabolic functions, thereby revealing its potential for cancer therapeutics. We have identified the most mutated functional domain of BACH1, the hot spot for tumorigenesis, justifying it as a target molecule in different cancer types for therapeutics. BACH1 has high potentials of transforming a normal cell into a tumor cell if compromised under certain circumstances. Thus, through this review, we justify BACH1 as an oncogene along with the existing role of being a tumor suppressant.

Effect of calcium glucoheptonate on proliferation and osteogenesis of osteoblast-like cells in vitro.

Calcium is the key macromineral having a role in skeletal structure and function, muscle contraction, and neurotransmission. Bone remodeling is maintained through a constant balance between calcium resorption and deposition. Calcium deficiency is resolved through calcium supplementation, and among the supplements, water-soluble organic molecules attracted great pharmaceutical interest. Calcium glucoheptonate is a highly water-soluble organic calcium salt having clinical use; however, detailed investigations on its biological effects are limited. We assessed the effects of calcium glucoheptonate on cell viability and proliferation of osteoblast-like MG-63 cells. Calcium uptake and mineralization were evaluated using Alizarin red staining of osteoblast-like MG-63 cells treated with calcium glucoheptonate. Expression of osteogenic markers were monitored by western blotting, immunofluorescence, and qRT-PCR assays. Increased proliferation and calcium uptake were observed in the MG-63 cells treated with calcium glucoheptonate. The treatment also increased the expression of osteopontin and osteogenic genes such as collagen-1, secreted protein acidic and cysteine rich (SPARC), and osteocalcin. Calcium glucoheptonate treatment did not exert any cytotoxicity on colorectal and renal epithelial cells, indicating the safety of the treatment. This is the first report with evidence for its beneficial effect for pharmaceutical use in addressing calcium deficiency conditions.

Fluctuating nonlinear hydrodynamics of flocking.

Starting from a microscopic model, the continuum field theoretic description of the dynamics of a system of active ingredients or "particles" is presented. The equations of motion for the respective collective densities of mass and momentum follow exactly from that of a single element in the flock. The single-particle dynamics has noise and anomalous momentum dependence in its frictional terms. The equations for the collective densities are averaged over a local equilibrium distribution to obtain the corresponding coarse grained equations of fluctuating nonlinear hydrodynamics (FNH). The latter are the equations used frequently for describing active systems on the basis of intuitive arguments. The transport coefficients which appear in the macroscopic FNH equations are determined in terms of the parameters of the microscopic dynamics.

Analysis of DNA Replication in Fission Yeast by Combing.

DNA replication studies based on population experiments give an average estimate of replication kinetics from many cells. This average replication profile masks the stochastic nature of origin firing in eukaryotes, which is revealed by using single-molecule techniques, such as DNA combing. The analysis of replication kinetics by DNA combing involves isolating DNA from cells that have been pulse-labeled with thymidine analogs and stretching it on a silanized coverslip. The analog-labeled patches on the stretched DNA fibers can then be detected using fluorescent antibodies against the analog. Each fiber represents a part of the genome from a single cell; therefore, it is possible to study the variation in behavior of individual origins from one cell to another. Furthermore, each DNA fiber is uniformly stretched, making it possible to measure distances accurately at kilobase resolution. It is also possible to stretch a high density of fibers on coverslips enabling quantitative data collection.

Open Navicular Dislocation With Midfoot Dissociation in a 45-Year-Old Man.

Traumatic dislocation of an intact tarsal navicular is an uncommon injury. In this article, we report a case of open medial navicular dislocation in a 45-year-old man. The injury was managed with open reduction and stabilization with Kirschner wires within the acute period. Ten months after injury, the patient developed avascular necrosis of the navicular and exhibited progressive collapse of the medial midfoot. He underwent naviculocuneiform arthrodesis 1 year after the index surgery. Two years after fusion, he was pain-free and ambulating independently. Successful treatment of midfoot fractures and dislocations requires an intimate understanding of anatomy, biomechanics, and both short- and long-term sequelae of injury.

Dependence of the configurational entropy on amorphous structures of a hard-sphere fluid.

The free energy of a hard-sphere fluid for which the average energy is trivial signifies how its entropy changes with packing. The packing η_{f} at which the free energy of the crystalline state becomes lower than that of the disordered fluid state marks the freezing point. For packing fractions η>η_{f} of the hard-sphere fluid, we use the modified weighted density functional approximation to identify metastable free energy minima intermediate between uniform fluid and crystalline states. The distribution of the sharply localized density profiles, i.e., the inhomogeneous density field ρ(x) characterizing the metastable state is primarily described by a pair function g_{s}(η/η_{0}). η_{0} is a structural parameter such that for η=η_{0} the pair function is identical to that for the Bernal random structure. The configurational entropy S_{c} of the metastable hard-sphere fluid is calculated by subtracting the corresponding vibrational entropy from the total entropy. The extrapolated S_{c} vanishes as η→η_{K} and η_{K} is in agreement with other works. The dependence of η_{K} on the structural parameter η_{0} is obtained.

How and why multiple MCMs are loaded at origins of DNA replication.

Recent work suggests that DNA replication origins are regulated by the number of multiple mini-chromosome maintenance (MCM) complexes loaded. Origins are defined by the loading of MCM - the replicative helicase which initiates DNA replication and replication kinetics determined by origin's location and firing times. However, activation of MCM is heterogeneous; different origins firing at different times in different cells. Also, more MCMs are loaded in G1 than are used in S phase. These aspects of MCM biology are explained by the observation that multiple MCMs are loaded at origins. Having more MCMs at early origins makes them more likely to fire, effecting differences in origin efficiency that define replication timing. Nonetheless, multiple MCM loading raises new questions, such as how they are loaded, where these MCMs reside at origins, and how their presence affects replication timing. In this review, we address these questions and discuss future avenues of research.

Linking density functional and mode coupling models for supercooled liquids.

We compare predictions from two familiar models of the metastable supercooled liquid, respectively, constructed with thermodynamic and dynamic approaches. In the so called density functional theory the free energy F[ρ] of the liquid is a functional of the inhomogeneous density ρ(r). The metastable state is identified as a local minimum of F[ρ]. The sharp density profile characterizing ρ(r) is identified as a single particle oscillator, whose frequency is obtained from the parameters of the optimum density function. On the other hand, a dynamic approach to supercooled liquids is taken in the mode coupling theory (MCT) which predict a sharp ergodicity-non-ergodicity transition at a critical density. The single particle dynamics in the non-ergodic state, treated approximately, represents a propagating mode whose characteristic frequency is computed from the corresponding memory function of the MCT. The mass localization parameters in the above two models (treated in their simplest forms) are obtained, respectively, in terms of the corresponding natural frequencies depicted and are shown to have comparable magnitudes.

Replication timing is regulated by the number of MCMs loaded at origins.

Replication timing is a crucial aspect of genome regulation that is strongly correlated with chromatin structure, gene expression, DNA repair, and genome evolution. Replication timing is determined by the timing of replication origin firing, which involves activation of MCM helicase complexes loaded at replication origins. Nonetheless, how the timing of such origin firing is regulated remains mysterious. Here, we show that the number of MCMs loaded at origins regulates replication timing. We show for the first time in vivo that multiple MCMs are loaded at origins. Because early origins have more MCMs loaded, they are, on average, more likely to fire early in S phase. Our results provide a mechanistic explanation for the observed heterogeneity in origin firing and help to explain how defined replication timing profiles emerge from stochastic origin firing. These results establish a framework in which further mechanistic studies on replication timing, such as the strong effect of heterochromatin, can be pursued.

Renormalized dynamics of the Dean-Kawasaki model.

We study the model of a supercooled liquid for which the equation of motion for the coarse-grained density ρ(x,t) is the nonlinear diffusion equation originally proposed by Dean and Kawasaki, respectively, for Brownian and Newtonian dynamics of fluid particles. Using a Martin-Siggia-Rose (MSR) field theory we study the renormalization of the dynamics in a self-consistent form in terms of the so-called self-energy matrix Σ. The appropriate model for the renormalized dynamics involves an extended set of field variables {ρ,θ}, linked through a nonlinear constraint. The latter incorporates, in a nonperturbative manner, the effects of an infinite number of density nonlinearities in the dynamics. We show that the contributing element of Σ which renormalizes the bare diffusion constant D(0) to D(R) is same as that proposed by Kawasaki and Miyazima [Z. Phys. B Condens. Matter 103, 423 (1997)]. D(R) sharply decreases with increasing density. We consider the likelihood of a ergodic-nonergodic (ENE) transition in the model beyond a critical point. The transition is characterized by the long-time limit of the density correlation freezing at a nonzero value. From our analysis we identify an element of Σ which arises from the above-mentioned nonlinear constraint and is key to the viability of the ENE transition. If this self-energy would be zero, then the model supports a sharp ENE transition with D(R)=0 as predicted by Kawasaki and Miyazima. With the full model having nonzero value for this self-energy, the density autocorrelation function decays to zero in the long-time limit. Hence the ENE transition is not supported in the model.

Ott1 (Rbm15) regulates thrombopoietin response in hematopoietic stem cells through alternative splicing of c-Mpl.

Thrombopoietin (Thpo) signaling through the c-Mpl receptor promotes either quiescence or proliferation of hematopoietic stem cells (HSCs) in a concentration-dependent manner; however, in vivo Thpo serum levels are responsive to platelet mass rather than HSC demands, suggesting additional regulation exists. Ott1 (Rbm15), a spliceosomal component originally identified as a fusion partner in t(1;22)-associated acute megakaryocytic leukemia, is also essential for maintaining HSC quiescence under stress. Ott1 controls the alternative splicing of a dominant negative isoform, Mpl-TR, capable of inhibiting HSC engraftment and attenuating Thpo signaling. Ott1, which associates with Hdac3 and the histone methyltransferase, Setd1b, binds to both c-Mpl RNA and chromatin and regulates H4 acetylation and H3K4me3 marks. Histone deacetylase or histone methyltransferase inhibition also increases Mpl-TR levels, suggesting that Ott1 uses an underlying epigenetic mechanism to control alternative splicing of c-Mpl. Manipulation of Ott1-dependent alternative splicing may therefore provide a novel pharmacologic avenue for regulating HSC quiescence and proliferation in response to Thpo.

Qualitatively different collective and single-particle dynamics in a supercooled liquid.

The equations of fluctuating nonlinear hydrodynamics for a two component mixture are obtained with a proper choice of slow variables which correspond to the conservation laws in the system. Using these nonlinear equations we construct the basic equations of the mode coupling theory (MCT) and consequent ergodic-nonergodic (ENE) transition in a binary mixture. The model is also analyzed in the one component limit of the mixture to study the dynamics of a tagged particle in the sea of identical particles. According to the existing MCT, dynamics of the single-particle correlation is slaved to that of the collective density fluctuations and, hence, both correlations freeze simultaneously at the ENE transition. We show here from a nonperturbative approach that at the ENE transition, characterized by the freezing of the long time limit of the dynamic correlation of collective density fluctuations to a nonzero value, the tagged-particle correlation still decays to zero. Our result implies that the point at which simulation or experimental data of the self-diffusion constant extrapolate to zero would not correspond to the ENE transition of simple MCT.

Slow dynamics of a tagged particle in a supercooled liquid.

The ergodicity-nonergodicity (ENE) transition of the self-consistent mode-coupling theory (MCT) is marked by the point at which the time correlation of collective density fluctuations is not zero in the long-time limit. The nonergodic state, reaching beyond the ENE transition of simple MCT, is characterized by a finite shear modulus. The MCT, formulated in the current set of papers, predicts that the single-particle density correlation, unlike the collective density correlation, decays to zero at long times on either side of the ENE transition. The self-diffusion coefficient remains finite. This differs from the existing MCT results in which both collective and single-particle correlations are simultaniously frozen at the ENE transition. We discuss in this paper mechanisms by which a sharp fall in self-diffusion coefficient may occur within the present model. This overdamping or the so-called adiabatic approximation for the supercooled state does not maintain microscopic momentum conservation. Within this approximation, the self-diffusion constant approaches zero at the ENE transition point. This approximate result, which is similar to the prediction of the existing MCT models, further illustrates the process of cage formation with increase of density. At a qualitative level, our analysis shows that the self-diffusion process depends on the structure as well as short-time transport properties of the supercooled liquid. We solve the integral equations for the nonergodicity parameters to analyze the full implications of the adiabatic approximation.