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Abstract Fundamental to all living organisms and living soft matter are emergent processes in which the reorganization of individual constituents at the nanoscale drives group-level movements and shape changes at the macroscale over time. However, light-induced degradation of fluorophores, photobleaching, is a significant problem in extended bioimaging in life science. Here, we report opening a long-time investigation window by nonbleaching phase intensity nanoscope: PINE. We accomplish phase-intensity separation such that nanoprobe distributions are distinguished by an integrated phase-intensity multilayer thin film (polyvinyl alcohol/liquid crystal). We overcame a physical limit to resolve sub-10 nm cellular architectures, and achieve the first dynamic imaging of nanoscopic reorganization over 250 h using PINE. We discover nanoscopic rearrangements synchronized with the emergence of group-level movements and shape changes at the macroscale according to a set of interaction rules with importance in cellular and soft matter reorganization, self-organization, and pattern formation.

Microtubules are cytoskeletal polymers of ⍺/β-tubulin heterodimers essential for a wide range of cellular processes. Pathogenic variations in microtubule-encoding genes (e.g., TUBB4B, which encodes the β-4B tubulin isotype) are responsible for a wide spectrum of cerebral malformations, collectively referred to as “tubulinopathies.” The phenotypic manifestation of TUBB4B-associated tubulinopathy is Leber congenital amaurosis with early-onset deafness (LCAEOD), an autosomal dominant syndrome characterized by photoreceptor and cochlear cell loss; all known patients have pathogenic variations in amino acid R391. We present the clinical and molecular genetics findings of a 16-year-old female with a de novo missense variant in exon 1 of TUBB4B, c.32 A > G (p.Gln11Arg; Q11R). In addition to hearing loss and hyperopia without retinal abnormalities, our proband presented with two phenotypes of unknown genetic etiology, i.e., renal tubular Fanconi Syndrome (FS) and hypophosphatemic rickets (HR). The Q11R variant expands the genetic basis of early sensory hearing loss; its consequences with respect to microtubule structure are described. A mechanistic explanation for the FS and rickets, involving microtubule-mediated translocation of transporter proteins to and from the apical membrane of renal proximal tubular cells, is proposed.

Kinesin force generation involves ATP-induced docking of the neck linker (NL) along the motor core. However, the roles of the proposed steps of NL docking, cover-neck bundle (CNB) and asparagine latch (N-latch) formation, during force generation are unclear. Furthermore, the necessity of NL docking for transport of membrane-bound cargo in cells has not been tested. We generated kinesin-1 motors impaired in CNB and/or N-latch formation based on molecular dynamics simulations. The mutant motors displayed reduced force output and inability to stall in optical trap assays but exhibited increased speeds, run lengths, and landing rates under unloaded conditions. NL docking thus enhances force production but at a cost to speed and processivity. In cells, teams of mutant motors were hindered in their ability to drive transport of Golgi elements (high-load cargo) but not peroxisomes (low-load cargo). These results demonstrate that the NL serves as a mechanical element for kinesin-1 transport under physiological conditions.

Asymmetric stem cell division is a critical mechanism for balancing self-renewal and differentiation. Adult stem cells often orient their mitotic spindle to place one daughter inside the niche and the other outside of it to achieve asymmetric division. It remains unknown whether and how the niche may direct division orientation. Here we discover a novel and evolutionary conserved mechanism that couples cell polarity to cell fate. We show that the cytokine receptor homolog Dome, acting downstream of the niche-derived ligand Upd, directly binds to the microtubule-binding protein Eb1 to regulate spindle orientation in Drosophila male germline stem cells (GSCs). Dome’s role in spindle orientation is entirely separable from its known function in self-renewal mediated by the JAK-STAT pathway. We propose that integration of two functions (cell polarity and fate) in a single receptor is a key mechanism to ensure an asymmetric outcome following cell division.

ABSTRACT The phosphoserine/phosphothreonine-binding protein 14-3-3 is known to regulate actin; this function has been previously attributed to sequestration of phosphorylated cofilin. 14-3-3 was identified as an actin-associated protein in the deep-branching eukaryote Giardia lamblia; however, Giardia lacks cofilin and all other canonical actin-binding proteins (ABPs). Thus, the role of G. lamblia 14-3-3 (Gl-14-3-3) in actin regulation was unknown. Gl-14-3-3 depletion resulted in an overall disruption of actin organization characterized by ectopically distributed short actin filaments. Using phosphatase and kinase inhibitors, we demonstrated that actin phosphorylation correlated with destabilization of the actin network and increased complex formation with 14-3-3, while blocking actin phosphorylation stabilized actin filaments and attenuated complex formation. Giardia’s sole Rho family GTPase, Gl-Rac, modulates Gl-14-3-3’s association with actin, providing the first connection between Gl-Rac and the actin cytoskeleton in Giardia. Giardia actin (Gl-actin) contains two putative 14-3-3 binding motifs, one of which (S330) is conserved in mammalian actin. Mutation of these sites reduced, but did not completely disrupt, the association with 14-3-3. Native gels and overlay assays indicate that intermediate proteins are required to support complex formation between 14-3-3 and actin. Overall, our results support a role for 14-3-3 as a regulator of actin; however, the presence of multiple 14-3-3–actin complexes suggests a more complex regulatory relationship than might be expected for a minimalistic parasite. IMPORTANCE Giardia lacks canonical actin-binding proteins. Gl-14-3-3 was identified as an actin interactor, but the significance of this interaction was unknown. Loss of Gl-14-3-3 results in ectopic short actin filaments, indicating that Gl-14-3-3 is an important regulator of the actin cytoskeleton in Giardia. Drug studies indicate that Gl-14-3-3 complex formation is in part phospho-regulated. We demonstrate that complex formation is downstream of Giardia’s sole Rho family GTPase, Gl-Rac. This result provides the first mechanistic connection between Gl-Rac and Gl-actin in Giardia. Native gels and overlay assays indicate intermediate proteins are required to support the interaction between Gl-14-3-3 and Gl-actin, suggesting that Gl-14-3-3 is regulating multiple Gl-actin complexes.

Aggregates of amyloid-beta (Aβ) peptides are thought to be involved in the development of Alzheimer's disease because they can change synaptic plasticity and induce neuronal cell death by inflammation, oxidative damage, and transmembrane pore formation. Exactly which oligomeric species underlie these cytotoxic effects remains unclear. The work presented here established well-controlled aggregation conditions of Aβ₁₋₄₀ or Aβ₁₋₄₂ peptides over a 20-day period and characterized these preparations with regard to their β-sheet content, degree of fibril formation, relative abundance of various oligomer sizes, and propensity to induce membrane pore formation and cytotoxicity. Using this multivariate data set, a systematic and inherently unbiased partial least squares (PLS) approach showed that for both peptides the abundance of oligomers in the tetramer to 13-mer range contributed positively to both pore formation and cytotoxicity, while monomers, dimers, trimers, and the largest oligomers (>210 kDa) were negatively correlated to both phenomena. Multivariate PLS analysis is ideally suited to handle complex data sets and interdependent variables such as relative oligomer concentrations, making it possible to elucidate structure function relationships in complex mixtures. This approach, therefore, introduces an enabling tool to the field of amyloid research, in which it is often difficult to interpret the activity of individual species within a complex mixture of bioactive species.

Apicomplexan parasites rely on a novel form of actin-based motility called gliding, which depends on parasite actin polymerization, to migrate through their hosts and invade cells. However, parasite actins are divergent both in sequence and function and only form short, unstable filaments in contrast to the stability of conventional actin filaments. The molecular basis for parasite actin filament instability and its relationship to gliding motility remain unresolved. We demonstrate that recombinant Toxoplasma (TgACTI) and Plasmodium (PfACTI and PfACTII) actins polymerized into very short filaments in vitro but were induced to form long, stable filaments by addition of equimolar levels of phalloidin. Parasite actins contain a conserved phalloidin-binding site as determined by molecular modeling and computational docking, yet vary in several residues that are predicted to impact filament stability. In particular, two residues were identified that form intermolecular contacts between different protomers in conventional actin filaments and these residues showed non-conservative differences in apicomplexan parasites. Substitution of divergent residues found in TgACTI with those from mammalian actin resulted in formation of longer, more stable filaments in vitro. Expression of these stabilized actins in T. gondii increased sensitivity to the actin-stabilizing compound jasplakinolide and disrupted normal gliding motility in the absence of treatment. These results identify the molecular basis for short, dynamic filaments in apicomplexan parasites and demonstrate that inherent instability of parasite actin filaments is a critical adaptation for gliding motility.

Pineapple, a popular tropical fruit with diverse culinary and health applications, has gained significant attention due to its economic importance, health benefits, and scientific exploration. Abiotic stress has been shown to have detrimental effects on physiological aspects of pineapple, such as photosynthesis rate and internal browning. However, physical and physiological parameters are inadequate in providing accurate assessment, early detection, and enabling marker-assisted breeding for pineapple under abiotic stress. Genetic markers provide valuable insights into plant defense mechanisms and stress tolerance, enabling the identification of key genes and pathways involved. The aim of this review was to discuss the potential of genetic markers as a reliable tool for studying abiotic stress in pineapple. It focuses on genes involved in stress response and their utility as genetic markers, while also discussing physiological changes. The responsiveness of several gene families, including CPK, CBL, CYS, Dof, TALE, SBP, WRKY, ZIP, R2R3-MYB, and DREB, to abiotic stress has been known before. Therefore, harnessing the potential of these genes can yield valuable insights for comprehending and effectively managing abiotic stress in pineapple. A comprehensive understanding of the genetic response to abiotic stress in pineapple is essential for enhancing agricultural productivity and developing stress-resistant varieties.

The presence of acidic soil in rural areas poses difficulties for agricultural production. One factor regulating soil pH is the overuse of inorganic fertilizer. The increased use of fertilizers in soybean production not only raises sustainability concerns but also contributes to soil acidity. Therefore, the use of organic fertilizer could offer a solution for addressing both issues related to soil acidity and sustainability. The purpose of this study was to investigate the manipulation of soil pH using organic fertilizer for soybean production under acidic stress. The planting medium, consisting of a mixture of topsoil, rice husk charcoal, and organic fertilizer (in a ratio of 2:1:1), was supplemented with 0.5 ​g of NPK fertilizer as a basal treatment in each planting medium. To regulate the soil acidity to pH 4, we added FeSO4 and allowed the mixture to incubate for 30 days. The results demonstrate that the application of three types of organic fertilizers chicken manure (P1), oil palm empty bunch fertilizer (P2), and vermicompost (P3) positively impacts the growth of three soybean varieties. The findings indicate that the application of P2 organic fertilizer can increase vegetative growth almost 50% in soybeans on acidic soil, including plant height, leaf count, and root length. Meanwhile, applying P3 organic fertilizer can boost reproductive growth responses in soybeans on acidic soil, such as pod number (from around 0-4 unit to 42–51 unit), grain number (from around 0-5 unit to 88–90 unit), and grain weight (from around 0–0.37 ​g to 12–25 ​g). Organic fertilizer has the potential to regulate soil pH, promoting higher yields of soybeans under acidic stress.

Effective catalysts for the thermal depolymerization of biomass present an attractive way to reduce energy consumption. This study investigated the effect of spent ZSM-5 catalysts on product distribution through thermal catalytic depolymerization. The spent catalyst has similar properties to the commercial fresh catalysts, as assessed through characterization analysis. The utilization of spent catalysts can enhance the production of bio-oil. The bio-oil yields for rice straw, brown solid, alkaline, and dealkaline lignin by catalytic depolymerization are 11%, 31%, 6%, and 21%, respectively. Therefore, depolymerization using a spent catalyst is a promising method to degrade lignocellulose.

Carbon capture and utilization are crucial parts of minimizing the negative impacts of climate change caused by CO2 emissions. Furthermore, Polyethylene terephthalate (PET) has emerged as the predominant option for beverage packaging and textile fiber on a global scale. Moreover, CO2 capture and utilization can be a great solution to produce PET feedstocks effectively, such as ethylene glycol (EG), terephthalic acid (TPA), and dimethyl. Several strategies have been used to obtain the raw materials for PET production through CO2 utilization, including EG production from ethylene carbonate, EG production from coal, TPA production from benzene, TPA production from p-xylene, and EG production by the electrochemical process. CO2 utilization is often used for chemical production and recycling. However, there is limited information available regarding CO2 utilization in PET production and recycling. This review presents CO2 utilization for PET raw material supply and recycling from an environmental sustainability standpoint.

Anggur merah (Vitis vinivera) adalah salah satu jenis buah yang banyak digemari masyarakat di Indonesia. Salah satu cara yang digunakan untuk menjaga mutu buah anggur merah adalah dengan pengaplikasikan bahan pelapis buah menggunakan kitosan. Penelitian ini dilakukan untuk mengetahui pengaruh pelapisan kitosan terhadap mutu buah anggur merah (Vitis vinivera). Penelitian ini dilakukan dengan variasi konsentrasi kitosan 2, 3, dan 4%. Setiap perlakuan menggunakan metode pencelupan selama 5 menit dan diamati selama 7 hari dengan waktu pengamatan hari ke 0, 3, dan 7. Hasil penelitian menunjukkan bahwa pelapisan kitosan dapat menyebabkan perubahan susut bobot dan tekstur selama penyimpanan, yang berpotensi digunakan sebagai pelapis untuk memperpanjang umur simpan anggur merah.

Kacang tanah (Arachis hypogea L.) merupakan komoditas kacang-kacangan utama di Indonesia karena memiliki sumber protein nabati dan nilai gizi yang tinggi. Salah satu faktor yang menghambat upaya peningkatan produksi kacang tanah yaitu minimnya benih yang bermutu tinggi yang dapat dipengaruhi oleh lama penyimpanan benih. Salah satu upaya yang dapat dilakukan untuk mengurangi rendahnya mutu suatu benih yaitu melakukan pengujian dini mutu benih. Penelitian ini bertujuan untuk mengetahui viabilitas benih kacang tanah varietas tuban dengan menggunakan uji tetrazolium dan daya berkecambah pada penyimpanan benih yang lama. Pengujian ini dilakukan dengan 2 metode yaitu uji tetrazolium dan uji daya berkecambah. Pengambilan sampel dilakukan dengan metode purposive sampling dengan 4 kali ulangan. Hasil penelitian menunjukkan bahwa terjadi penurunan viabilitas benih kacang tanah yang disimpan selama 1 tahun, dari 86% turun mencapai 34%, dengan kondisi kadar air meningkat dari 6.8% menjadi 7.4%. Selain itu, hasil uji daya berkecambah benih kacang tanah ditemukan sebanyak 34% normal, 45% kecambah abnormal dan 21% kecambah mati. Berdasarkan uji tetrazolium, ditemukan bahwa benih yang viabel sebesar 79% dan benih non viabel sebesar 21%. Hasil ini menunjukkan bahwa perlu adanya upaya peningkatan viabilitas dan daya berkecambah benih kacang tanah varietas tuban. Identifikasi awal kualitas benih merupakan hal yang penting bagi para pelaku usaha tani agar terhindar dari kegagalan panen.

Maize is one of important comodities contributed as food consumption and other bioproducts to the world. As high demand of maize in global must be followed its avalaibility in markets. Decline the post-harvest losses along maize distribution will not only keep the avalaibility in markets, but also solve the food security. One of post-harvest losses causes is pest, especially in maize storage. The temperature treatment to control S.zeamais, a major insect found in maize storage, becomes potential action in order to reduces the post-harvest losses. The aim of this study was to investigate the S.zeamais mortality rate and physical changes of maize kernel under low temperature condition. The S.zeamais was cultured within 4 months before used for experiments. The 2 different low temperature conditions and 1 control treatment were used in this study. The results showed that the temperature of maize kernel was changed, indicated the movement of maize from room temperature to low temperature storage is occurred. Furthermore, the low temperature treatments, the maize moisture content was slightly changed compared to the control treatment. In addition, there is no chilling injury issue to maize kernel. However, the unknown mechanism of S.zeamais protection to the low temperature was found in the Low Temperature I treatment through the finding of hole grain. In the mortality rate, the highest mortality rate was found at Low Temperature II treatment (95.30 ±11.54%). These findings suggests that low temperature treatment could be the action for maize pest management, especially in the storage.

Agricultural activity relies on soil as their growth media. Besides agricultural activity, other living species also needs soil as their ecosystem. However, the biodiversity and environmental factor are often neglected in agricultural activity. Therefore, the investigation of environmental and biodiversity changes is important. In this study, the environmental parameter and biodiversity changes was investigated in area after land clearing activity. The pH was increased from in 3 times measurement. Besides, the soil temperature and air temperature was also increased in 3 times measurement between pre- and post-treatment. The soil temperature ranges from 26.2 oC to 33.2 oC in pre-treatment and 27.6 oC to 31.8 oC in post-treatment. The air temperature was observed ranges from 27.96 oC to 34.3 oC in pre-treatment and 28.36 oC to 34.56 oC in post-treatment. Measurement of RH was resulted ranges from 61.2% to 75.4% in pre-treatment and 61.4% to 74.8% in pre-treatment. The land is proposed become paddy field for next step land processing. As result, the diversity index was decreased in pre- and post-treatment. The Shannon diversity index was decreased from 0.81 to 0.72. Similarly, the Simpson diversity index was also decreased from 1.94 to 1.77. Meanwhile, the evenness index was increased from 0.58 to 0.65. These results suggested for farmer to process the land as soon as possible after land clearing process, if they want to form paddy field from pasture land. Abstrak Kegiatan pertanian bergantung pada tanah sebagai media tumbuh suatu tanaman. Selain kegiatan pertanian, organisme hidup lain juga bergantung terhadap tanah sebagai ekosistem. Namun, seringkali biodiversitas dan faktor lingkungan diabaikan dalam kegiatan pertanian. Oleh karenanya, indentifikasi perubahan lingkungan dan biodiversitas sanget perlu dilakukan. Dalam penelitian ini, perubahan parameter lingkungan dan biodiversitas diamati sebelum dan sesudah aktivitas land clearing. Hasil pengamatan menunjukkan, pH tanah, suhu tanah dan suhu lingkungan meningkat dalam 3 kali pengukuran dari sebelum ke sesudah aktivitas land clearing. Suhu tanah berkisar 26.2 oC-33.2 oC pada sebelum kegiatan land clearing dan 27.6 oC-31.8 oC setelah aktivitas land clearing. Suhu lingkungan ditemukan berkisar 27.96 oC-34.3 oC pada kegiatan sebelum land clearing dan 28.36 oC-34.56 oC setelah kegiatan land clearing. Hasil pengukuran RH lingkungan ditemukan berkisar 61.2%-75.4% pada kegiatan sebelum land clearing dan 61.4%-74.8% setelah kegiatan land clearing. Sementara itu, index diversitas ditemukan menurun setelah aktivitas land clearing. Nilai Shannon diversity index ditemukan menurun setelah aktivitas land clearing dari 0.81-0.72. Pola serupa ditemukan pada nilai Simpson diversity index, dimana terjadi penurunan dari 1.94 menjadi 1.77. Nilai evenness index meningkat dari 0.58 menjadi 0.65. Berdasarkan hasil tersebut dapat disarankan ke petani untuk segera mengolah lahan tersebut setelah kegiatan land clearing untuk menghindari terjadinya pertumbuhan kembali vegetasi, serta perubahan parameter lingkungan dan biodiversitas.

Banana is tropical fruit contain health nutrition and fiber. Dwarf banana is one of type banana that well growth in Indonesia, particularly in Lampung Province. However, its economic value become exported commodities is limited by its short shelf life. In this study, the physicochemical changes were observed under vacuum packaging storage, in order to know the potency of vacuum packaging to prolong the shelf life of dwarf banana. The results showed that the vacuum packaging could reduce weight loss compare to other treatments. The maintenance of green color by vacuum packaging was also showed positive result. Furthermore, the dwarf banana under vacuum packaging storage was also showed lowest TSS, in other words, the dwarf maturity could be delayed. These results suggested the vacuum packaging could be used as potential packaging for dwarf banana.

The four transcription factors OCT4, SOX2, KLF4 and c-MYC are highly expressed in embryonic stem cells (ESC) and their overexpression can induce pluripotency, the ability to differentiate into all cell types of an organism. The ectopic expression such transcription factors could reprogram somatic stem cells become induced pluripotency stem cells (iPSC), an embryonic stem cells-like. Production of recombinant pluripotency factors gain interests due to high demand from generation of induced pluripotent stem cells in regenerative medical therapy recently. This review will focus on demonstrate the recent advances in recombinant pluripotency factor production using various host.

Zanthoxylum acanthopodium, locally known as Andaliman, is exotic spices which grown in North Sumatera. Several investigation shown that the special taste and aroma comes from pericarp of Andaliman. However, the pericarp of Andaliman is easily degraded. The proper postharvest handling of Andaliman is necessary to preserve fresh Andaliman for long time. Previously, Andaliman has been preserved in packaging under room temperature storage. Further investigation of Andaliman preservation in packaging under low temperature storage would help reduces the postharvest losses. In this study, the physical changes of Andaliman in various packaging under low-temperature storage were observed. The results shown that within 2 days, the pericarp of Andaliman in paper packaging was shrunk, similarly found in control without packaging. Meanwhile, the pericarp of Andaliman in aluminum foil and PP plastic were found normal in day 3. This result indicated that in low-temperature, Andaliman in Aluminum foil was recommended for best postharvest handling.