Plasticity of an ultrafast interaction between nucleoporins and nuclear transport receptors.

The mechanisms by which intrinsically disordered proteins engage in rapid and highly selective binding is a subject of considerable interest and represents a central paradigm to nuclear pore complex (NPC) function, where nuclear transport receptors (NTRs) move through the NPC by binding disordered phenylalanine-glycine-rich nucleoporins (FG-Nups). Combining single-molecule fluorescence, molecular simulations, and nuclear magnetic resonance, we show that a rapidly fluctuating FG-Nup populates an ensemble of conformations that are prone to bind NTRs with near diffusion-limited on rates, as shown by stopped-flow kinetic measurements. This is achieved using multiple, minimalistic, low-affinity binding motifs that are in rapid exchange when engaging with the NTR, allowing the FG-Nup to maintain an unexpectedly high plasticity in its bound state. We propose that these exceptional physical characteristics enable a rapid and specific transport mechanism in the physiological context, a notion supported by single molecule in-cell assays on intact NPCs.

Comparative analysis of the coordinated motion of Hsp70s from different organelles observed by single-molecule three-color FRET.

Cellular function depends on the correct folding of proteins inside the cell. Heat-shock proteins 70 (Hsp70s), being among the first molecular chaperones binding to nascently translated proteins, aid in protein folding and transport. They undergo large, coordinated intra- and interdomain structural rearrangements mediated by allosteric interactions. Here, we applied a three-color single-molecule Förster resonance energy transfer (FRET) combined with three-color photon distribution analysis to compare the conformational cycle of the Hsp70 chaperones DnaK, Ssc1, and BiP. By capturing three distances simultaneously, we can identify coordinated structural changes during the functional cycle. Besides the known conformations of the Hsp70s with docked domains and open lid and undocked domains with closed lid, we observed additional intermediate conformations and distance broadening, suggesting flexibility of the Hsp70s in adopting the states in a coordinated fashion. Interestingly, the difference of this distance broadening varied between DnaK, Ssc1, and BiP. Study of their conformational cycle in the presence of substrate peptide and nucleotide exchange factors strengthened the observation of additional conformational intermediates, with BiP showing coordinated changes more clearly compared to DnaK and Ssc1. Additionally, DnaK and BiP were found to differ in their selectivity for nucleotide analogs, suggesting variability in the recognition mechanism of their nucleotide-binding domains for the different nucleotides. By using three-color FRET, we overcome the limitations of the usual single-distance approach in single-molecule FRET, allowing us to characterize the conformational space of proteins in higher detail.

Nucleoporin-mediated regulation of cell identity genes.

The organization of the genome in the three-dimensional space of the nucleus is coupled with cell type-specific gene expression. However, how nuclear architecture influences transcription that governs cell identity remains unknown. Here, we show that nuclear pore complex (NPC) components Nup93 and Nup153 bind superenhancers (SE), regulatory structures that drive the expression of key genes that specify cell identity. We found that nucleoporin-associated SEs localize preferentially to the nuclear periphery, and absence of Nup153 and Nup93 results in dramatic transcriptional changes of SE-associated genes. Our results reveal a crucial role of NPC components in the regulation of cell type-specifying genes and highlight nuclear architecture as a regulatory layer of genome functions in cell fate.

Codon Usage Provide Insights into the Adaptation of Rice Genes under Stress Condition.

Plants experience different stresses, i.e., abiotic, or biotic, and to combat them, plants re-program the expression of growth-, metabolism-, and resistance-related genes. These genes differ in their synonymous codon usage frequency and show codon usage bias. Here, we investigated the correlation among codon usage bias, gene expression, and underlying mechanisms in rice under abiotic and biotic stress conditions. The results indicated that genes with higher expression (up- or downregulated) levels had high GC content (≥60%), a low effective number of codon usage (≤40), and exhibited strong biases towards the codons with C/G at the third nucleotide position, irrespective of stress received. TTC, ATC, and CTC were the most preferred codons, while TAC, CAC, AAC, GAC, and TGC were moderately preferred under any stress (abiotic or biotic) condition. Additionally, downregulated genes are under mutational pressure (R2 ≥ 0.5) while upregulated genes are under natural selection pressure (R2 ≤ 0.5). Based on these results, we also identified the possible target codons that can be used to design an optimized set of genes with specific codons to develop climate-resilient varieties. Conclusively, under stress, rice has a bias towards codon usage which is correlated with GC content, gene expression level, and gene length.

A systematic review on potential microbial carbohydrases: current and future perspectives.

Various studies have shown that the microbial proteins are often more stable than belongs to other sources like plant and animal origin. Hence, the interest in microbial enzymes has gained much attention due to many potential applications like bioenergy, biofuel production, biobleaching, bioconversion and so on. Additionally, recent trends revealed that the interest in isolating novel microbes from harsh environments have been the main focus of many scientists for various applications. Basically, industrially important enzymes can be categorized into mainly three groups: carbohydrases, proteases, and lipases. Among those, the enzymes especially carbohydrases involved in production of sugars. Carbohydrases include amylases, xylanases, pectinases, cellulases, chitinases, mannases, laccases, ligninases, lactase, glucanase, and glucose oxidase. Thus, here, an approach has been made to highlight five enzymes namely amylase, cellulase, laccase, pectinase, and xylanase from different sources with special emphasis on their properties, mechanism, applications, production optimization, purification, molecular approaches for its enhanced and stable production, and also biotechnological perspectives of its future development. Also, green and sustainable catalytic conversion strategies using nanoparticles of these enzymes have also been discussed. This review will provide insight into the carbohydrases importance and their usefulness that will help to the researchers working in this field.

Mathematical modeling and analysis for controlling the spread of infectious diseases.

In this work, we present and discuss the approaches, that are used for modeling and surveillance of dynamics of infectious diseases by considering the early stage asymptomatic and later stage symptomatic infections. We highlight the conceptual ideas and mathematical tools needed for such infectious disease modeling. We compute the basic reproduction number of the proposed model and investigate the qualitative behaviours of the infectious disease model such as, local and global stability of equilibria for the non-delayed as well as delayed system. At the end, we perform numerical simulations to validate the effectiveness of the derived results.

VOCs-mediated hormonal signaling and crosstalk with plant growth promoting microbes.

In the natural environment, plants communicate with various microorganisms (pathogenic or beneficial) and exhibit differential responses. In recent years, research on microbial volatile compounds (MVCs) has revealed them to be simple, effective and efficient groups of compounds that modulate plant growth and developmental processes. They also interfere with the signaling process. Different MVCs have been shown to promote plant growth via improved photosynthesis rates, increased plant resistance to pathogens, activated phytohormone signaling pathways, or, in some cases, inhibit plant growth, leading to death. Regardless of these exhibited roles, the molecules responsible, the underlying mechanisms, and induced specific metabolic/molecular changes are not fully understood. Here, we review current knowledge on the effects of MVCs on plants, with particular emphasis on their modulation of the salicylic acid, jasmonic acid/ethylene, and auxin signaling pathways. Additionally, opportunities for further research and potential practical applications presented.

Continuous throughput and long-term observation of single-molecule FRET without immobilization.

We present an automated microfluidic platform that performs multisecond observation of single molecules with millisecond time resolution while bypassing the need for immobilization procedures. With this system, we confine biomolecules to a thin excitation field by reversibly collapsing microchannels to nanochannels. We demonstrate the power of our method by studying a variety of complex nucleic acid and protein systems, including DNA Holliday junctions, nucleosomes and human transglutaminase 2.

The Development of Simple Methods for the Maintenance and Quantification of Polymyxa graminis.

Polymyxa graminis, a root endoparasite of several cereal species, is considered to be non-pathogenic but serves as a vector of various plant viruses belonging to the genera Bymovirus, Furovirus, and Pecluvirus. Specifically, it reduces barley productivity by transmitting the Barley Yellow Mosaic Virus (BaYMV). To date, due to its obligate biotrophic property, no artificial culturing of P. graminis was reported and its quantification was also technically challenging. Here, we developed a novel and simple method to infect P. graminis within sterile barley roots in contamination free by preparing nearly pure zoospore inoculum. Such artificial maintenance of P. graminis was verified based on the presence of various developmental stages in infected barley roots under microscope. In addition, the population of resting spores in host tissue was determined by establishing standard curve between manually counted number of spores and Ct values of 18S rDNA amplification using quantitative real-time PCR. Furthermore, it was validated that standard curve generated was also applicable to estimate the abundance of P. graminis in soil environments. In conclusion, the present study would help to generate a system to investigate the etiological causes as well as management of plant diseases caused by P. graminis and BaYMV in tissue and soil.

Protein Engineering in Cyanobacterial Biotechnology: Tools and Recent Updates.

Cyanobacteria have emerged as a microbial cell factory to produce a variety of bioproducts, including peptides and proteins. Cyanobacteria stand out among other organisms due to their photoautotrophic metabolism and ability to produce a wide range of metabolites. As photoautotrophic hosts can produce industrial compounds and proteins by using minimal resources such as sunlight, atmospheric carbon dioxide, and fewer nutrients, cyanobacteria are cost-effective industrial hosts. Therefore, the use of protein engineering tools for rational protein design, and the desired modification of enzyme activity has become a desirable undertaking in cyanobacterial biology. Protein engineering can improve their biological functions as well as the stability of their intracellular proteins. This review aims to highlight the success of protein engineering in the direction of cyanobacterial biotechnology and outlines the emerging technologies, current challenges, and prospects of protein engineering in cyanobacterial biotechnology.

Primary sclerosing encapsulating peritonitis.

Sclerosing encapsulating peritonitis also known as cocoon abdomen is a rare chronic inflammatory condition of the peritoneum in which the bowel loops are encircled by a membrane (cocoon formation) within the peritoneal cavity leading to intestinal obstruction. It can be primary (idiopathic) or secondary (chemotherapy, beta-blockers, peritoneal dialysis, shunts, tuberculosis, systemic lupus erythematosus, etc.). The symptomatology report includes recurrent episodes of abdominal pain and vomiting. We present here a case of a 32-year-old male who presented with complaints of being unable to pass stools, vomiting (3-4 times), and abdomen pain for 4 days. This case is considered worth mentioning due to its rarity, lack of identification of secondary causes, and diminutive mention of histopathological aspect.

How 'eye' helped in von Hippel-Lindau syndrome.

BACKGROUND: Von Hippel-Lindau syndrome is a rare autosomal dominantly inherited multisystemic oncologic syndrome, presenting predominantly with angiomatosis in embryologically similar neurologic tissue such as retina, cerebellum and adrenals. Retinal hemangioblastomas are the hallmark ophthalmic finding. In this case report, we describe the importance of timely diagnosis, thorough systemic examination and treatment of bilaterally asymmetrical retinal hemangioblastomas in a young adult male. CASE PRESENTATION: A 31-year-old male presented with painless diminution of vision in both eyes, associated with eyestrain and headache. Multiple asymmetric retinal lesions and dilated feeder vessels were noted on ophthalmoscopic examination and confirmed by fluorescein angiography to be retinal hemangioblastomas. Comprehensive systemic examination revealed cerebellar hemangioblastomas and multiple pancreatic and renal cysts. Treatment of retinal lesions was done by combination therapy of argon laser photocoagulation and cryopexy, which lead to a good visual outcome. Subsequently, neurosurgical resection of cerebellar hemangioblastoma proved to be lifesaving for the patient. CONCLUSION: RHBs are the earliest, easiest and the most frequently detected manifestation of VHL. Identification of ocular manifestations play a pivotal role in early diagnosis and timely intervention in VHL syndrome, thereby significantly reducing associated morbidity and mortality. Therefore, an ophthalmologist's role is crucial in the management of these potentially deadly tumours.

Pathways to the first contact with mental health services among patients with schizophrenia: A cross-sectional observational study.

Background: Schizophrenia is a mental illness with a profound impact on patient and their caregivers. There is increasing evidence that delay in the commencement of treatment following the onset of illness may be related to the pathways; patients navigate before accessing mental health services. Aim: The aim of this study is to assess the pathways of care to the first contact with mental health services among patients with schizophrenia. Methods: A total of 150 diagnosed schizophrenia patients aged 12-60 years were recruited as per inclusion and exclusion criteria. The sociodemographic details were gathered using semistructured sociodemographic data sheets; semistructured pathways to care questionnaire and positive and negative syndrome scale for schizophrenia were administered. Results: The most common first pathway to care was faith healers. The education of the head of family, socioeconomic status, rural background, and occupational status of patients have a significant impact on the first pathway of psychiatric care. The findings suggest that while planning mental health services, emphasis should be made on collaboration between psychiatric and nonpsychiatric services. Conclusion: The pathways patient choose depend on a number of factors like their socio-cultural background, belief about the supernatural causation of psychiatric illness, stigma associated with psychiatric illness, lack of knowledge about the mental illness, and influence of close family relatives on the choice of treatment.

Stature estimation from the scapula measurements using 3D-volume rendering technique by regression equations in the Northern Indian population.

The present study assessed the correlation between the stature and scapular measurements from both sides in order to develop population-specific regression equations to estimate the stature from measurements of the scapula in a contemporary Northern Indian population individually for the left and right sides. A total of 597 cadavers underwent postmortem multidetector computed tomography and subsequent medicolegal autopsy in our department between August 2021 and August 2022. Two hundred samples (100 males and 100 females) were randomly collected based on inclusion and exclusion criteria. Six linear anthropometric measurements of the scapula from either side were measured using the 3D volume-rendered technique by an electronic cursor. Each anthropometric measurement showed a significant difference between males and females (p < 0.05). Regression analysis was applied to match the taken measurements against stature. The accuracy to predict stature ranged from 3.99 to 4.94 cm for males and from 4.49 to 5.27 cm for females, respectively. Left-sided measurements were better predictors of stature than the right side in both genders. The results of this study indicate that scapular measurements could be useful to estimate the stature of Northern Indian individuals, particularly in scenarios of disaster victim identification lacking long bones, which are considered to be better predictors to date.

Click strategies for single-molecule protein fluorescence.

Single-molecule methods have matured into central tools for studies in biology. Foerster resonance energy transfer (FRET) techniques, in particular, have been widely applied to study biomolecular structure and dynamics. The major bottleneck for a facile and general application of these studies arises from the need to label biological samples site-specifically with suitable fluorescent dyes. In this work, we present an optimized strategy combining click chemistry and the genetic encoding of unnatural amino acids (UAAs) to overcome this limitation for proteins. We performed a systematic study with a variety of clickable UAAs and explored their potential for high-resolution single-molecule FRET (smFRET). We determined all parameters that are essential for successful single-molecule studies, such as accessibility of the probes, expression yield of proteins, and quantitative labeling. Our multiparameter fluorescence analysis allowed us to gain new insights into the effects and photophysical properties of fluorescent dyes linked to various UAAs for smFRET measurements. This led us to determine that, from the extended tool set that we now present, genetically encoding propargyllysine has major advantages for state-of-the-art measurements compared to other UAAs. Using this optimized system, we present a biocompatible one-step dual-labeling strategy of the regulatory protein RanBP3 with full labeling position freedom. Our technique allowed us then to determine that the region encompassing two FxFG repeat sequences adopts a disordered but collapsed state. RanBP3 serves here as a prototypical protein that, due to its multiple cysteines, size, and partially disordered structure, is not readily accessible to any of the typical structure determination techniques such as smFRET, NMR, and X-ray crystallography.

Sudden death of an egg donor during oocyte retrieval due to ovarian hyperstimulation syndrome.

Ovarian Hyperstimulation Syndrome (OHSS) is uncommon among oocyte donors during in vitro fertilization (IVF) procedure and is rarely associated with death. We report a case of a 23-year-old oocyte donor who suddenly died on the operation table during oocyte retrieval. She had no risk factors in her menstrual history, laboratory, or clinical parameters. The antagonist cycle, triggered with the GnRH agonist protocol, was carried out. The cause of death at autopsy was attributed to respiratory failure due to acute massive pulmonary edema, which developed due to the complication of OHSS. Only a few autopsy cases associated with OHSS have been published, but, as far as we know, no clinical or autopsy cases of sudden death caused by OHSS have been reported.

Co-inoculation of biochar and arbuscular mycorrhizae for growth promotion and nutrient fortification in soybean under drought conditions.

Drought is significant abiotic stress that affects the development and yield of many crops. The present study is to investigate the effect of arbuscular mycorrhizal fungi (AMF) and biochar on root morphological traits, growth, and physiological traits in soybean under water stress. Impact of AMF and biochar on development and root morphological traits in soybean and AMF spores number and the soil enzymes' activities were studied under drought conditions. After 40 days, plant growth parameters were measured. Drought stress negatively affected soybean growth, root parameters, physiological traits, microbial biomass, and soil enzyme activities. Biochar and AMF individually increase significantly plant growth (plant height, root dry weight, and nodule number), root parameters such as root diameter, root surface area, total root length, root volume, and projected area, total chlorophyll content, and nitrogen content in soybean over to control in water stress. In drought conditions, dual applications of AMF and biochar significantly enhanced shoot and root growth parameters, total chlorophyll, and nitrogen contents in soybean than control. Combined with biochar and AMF positively affects AMF spores number, microbial biomass, and soil enzyme activities in water stress conditions. In drought stress, dual applications of biochar and AMF increase microbial biomass by 28.3%, AMF spores number by 52.0%, alkaline phosphomonoesterase by 45.9%, dehydrogenase by 46.5%, and fluorescein diacetate by 52.2%, activities. The combined application of biochar and AMF enhance growth, root parameters in soybean and soil enzyme activities, and water stress tolerance. Dual applications with biochar and AMF benefit soybean cultivation under water stress conditions.

Study of dynamic behaviour of psychological stress during COVID-19 in India: A mathematical approach.

In this study, a new attempt has been made using mathematical modelling to study dynamic behaviour and estimate the final size of spread of the psychological stress arising due to sudden outbreak of COVID-19 in India. The proposed mathematical model examines and includes different behaviours of transition from one process to another in current situation and study their propagation mode. We propose a mathematical model, where two different type of psychological stresses occur due to COVID-19 situation and its impact on people's life such as their mental well being and happiness. We present some sufficient conditions for the vanishing or spreading of the psychological stress through qualitative and quantitative analysis. The basic reproduction number ( R 0 ) of the model is computed and the local and the global stabilities of different equilibria are studied. Moreover, to better understand the level of psychological stress and decreasing mental well-being during the COVID-19 outbreak in India, we also conducted an online survey. Our findings establish several factors associated with level of psychological impact and mental health status. Based on the empirical analysis, we found that psychological stress has a significant negative influence on mental well being. Further, this study confirms that coping strategies with stress have significantly contributed towards the betterment in the mental well-being of the people. Numerical simulations are also given to illustrate the theoretical results. The results of the present study can be generalized to the society, Government, and others that they can adopt different strategies to avoid stressful situations during COVID-19 outbreak. The findings suggest that policy-makers, Government officials should focus on coping strategies to combat with pandemic disease.

Engineering disease resistant plants through CRISPR-Cas9 technology.

Plants are susceptible to phytopathogens, including bacteria, fungi, and viruses, which cause colossal financial shortfalls (pre- and post-harvest) and threaten global food safety. To combat with these phytopathogens, plant possesses two-layer of defense in the form of PAMP-triggered immunity (PTI), or Effectors-triggered immunity (ETI). The understanding of plant-molecular interactions and revolution of high-throughput molecular techniques have opened the door for innovations in developing pathogen-resistant plants. In this context, Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-CRISPR-associated protein 9 (Cas9) has transformed genome editing (GE) technology and being harnessed for altering the traits. Here we have summarized the complexities of plant immune system and the use of CRISPR-Cas9 to edit the various components of plant immune system to acquire long-lasting resistance in plants against phytopathogens. This review also sheds the light on the limitations of CRISPR-Cas9 system, regulation of CRISPR-Cas9 edited crops and future prospective of this technology.