Dark fermentation on biohydrogen production: Pure culture

Biohydrogen is regarded as an attractive future clean energy carrier due to its high energy content and environmental-friendly conversion. While biohydrogen production is still in the early stage of development, there have been a variety of laboratory- and pilot-scale systems developed with promising potential. This work presents a review of literature reports on the pure hydrogen-producers under anaerobic environment. Challenges and perspective of biohydrogen production with pure cultures are also outlined.     

Aerobic granular sludge: recent advances

Aerobic granulation, a novel environmental biotechnological process, was increasingly drawing interest of researchers engaging in work in the area of biological wastewater treatment. Developed about one decade ago, it was exciting research work that explored beyond the limits of aerobic wastewater treatment such as treatment of high strength organic wastewaters, bioremediation of toxic aromatic pollutants including phenol, toluene, pyridine and textile dyes, removal of nitrogen, phosphate, sulphate and nuclear waste and adsorption of heavy metals. Despite this intensive research the mechanisms responsible for aerobic granulation and the strategy to expedite the formation of granular sludge, and effects of different operational and environmental factors have not yet been clearly described. This paper provides an up-to-date review on recent research development in aerobic biogranulation technology and applications in treating toxic industrial and municipal wastewaters. Factors affecting granulation, granule characterization, granulation hypotheses, effects of different operational parameters on aerobic granulation, response of aerobic granules to different environmental conditions, their applications in bioremediations, and possible future trends were delineated. The review attempts to shed light on the fundamental understanding in aerobic granulation by newly employed confocal laser scanning microscopic techniques and microscopic observations of granules.     

Extractive disruption process integration using ultrasonication and an aqueous two‐phase system for protein recovery from Chlorella sorokiniana

Microalgae emerge as the most promising protein sources for aquaculture industry. However, the commercial proteins production at low cost remains a challenge. The process of harnessing microalgal proteins involves several steps such as cell disruption, isolation and extraction. The discrete processes are generally complicated, time‐consuming and costly. To date, the notion of integrating microalgal cell disruption and proteins recovery process into one step is yet to explore. Hence, this study aimed to investigate the feasibility of applying methanol/potassium ATPS in the integrated process for proteins recovery from Chlorella sorokiniana. Parameters such as salt types, salt concentrations, methanol concentrations, NaCl addition were optimized. The possibility of upscaling and the effectiveness of recycling the phase components were also studied. The results showed that ATPS formed by 30% (w/w) K₃PO₄ and 20% (w/w) methanol with 3% (w/w) NaCl addition was optimum for proteins recovery. In this system, the partition coefficient and yield were 7.28 and 84.23%, respectively. There were no significant differences in the partition coefficient and yield when the integrated process was upscaled to 100‐fold. The recovered phase components can still be recycled effectively at fifth cycle. In conclusions, this method is simple, rapid, environmental friendly and could be implemented at large scale.     

Statistical discovery of site inter-dependencies in sub-molecular hierarchical protein structuring

Background

Much progress has been made in understanding the 3D structure of proteins using methods such as NMR and X-ray crystallography. The resulting 3D structures are extremely informative, but do not always reveal which sites and residues within the structure are of special importance. Recently, there are indications that multiple-residue, sub-domain structural relationships within the larger 3D consensus structure of a protein can be inferred from the analysis of the multiple sequence alignment data of a protein family. These intra-dependent clusters of associated sites are used to indicate hierarchical inter-residue relationships within the 3D structure. To reveal the patterns of associations among individual amino acids or sub-domain components within the structure, we apply a k-modes attribute (aligned site) clustering algorithm to the ubiquitin and transthyretin families in order to discover associations among groups of sites within the multiple sequence alignment. We then observe what these associations imply within the 3D structure of these two protein families.

Results

The k-modes site clustering algorithm we developed maximizes the intra-group interdependencies based on a normalized mutual information measure. The clusters formed correspond to sub-structural components or binding and interface locations. Applying this data-directed method to the ubiquitin and transthyretin protein family multiple sequence alignments as a test bed, we located numerous interesting associations of interdependent sites. These clusters were then arranged into cluster tree diagrams which revealed four structural sub-domains within the single domain structure of ubiquitin and a single large sub-domain within transthyretin associated with the interface among transthyretin monomers. In addition, several clusters of mutually interdependent sites were discovered for each protein family, each of which appear to play an important role in the molecular structure and/or function.

Conclusions

Our results demonstrate that the method we present here using a k- modes site clustering algorithm based on interdependency evaluation among sites obtained from a sequence alignment of homologous proteins can provide significant insights into the complex, hierarchical inter-residue structural relationships within the 3D structure of a protein family.

     

Recent Progress in Harvest and Recovery Techniques of Mammalian and Algae Cells for Industries

In our modern world, biotechnology products play important roles not only in our health and culture, but also various industries such as food, agriculture, sewage treatment, biofuels, nutraceuticals, and pharmaceuticals. Rapid technological advances in biotechnology over the last few decades have allowed industrial integration of mammalian cells (like the Chinese hamster ovary cells) and algae cells in pharmaceutical and biofuel industries to produce commercial products and valuable biomolecules. However, the cost of cell harvest and recovery can become expensive depending on the harvesting technique, degree of purification, and intended use of the end-products. This has led to numerous research in exploring and developing efficient harvesting techniques. Therefore, in this review, the popular harvesting techniques and their recent applications will be discussed.     

Anaerobic granulation technology for wastewater treatment

Anaerobic wastewater treatment using granular sludge reactors is a developing technology, in which granular sludge is the core component. So far, around 900 anaerobic granular sludge units have been operated worldwide. Although intensive research attention has been given to anaerobic granules in the past 20 years, the mechanisms responsible for anaerobic granulation and the strategy of how to expedite substantially the formation of granular sludge have not yet been completely clear. This paper reviews the mode of anaerobic granulation, including the mechanisms and models for anaerobic granulation, major factors influencing anaerobic granulation, characteristics of anaerobic granules, anaerobic granulation in other types of reactors, industrial application of anaerobic granulation technology and neural fuzzy model-based control strategy developed for anaerobic systems. Some approaches for future research are outlined.     

Intra-tumor genetic heterogeneity and alternative driver genetic alterations in breast cancers with heterogeneous HER2 gene amplification

BackgroundHER2 is overexpressed and amplified in approximately 15% of invasive breast cancers, and is the molecular target and predictive marker of response to anti-HER2 agents. In a subset of these cases, heterogeneous distribution of HER2 gene amplification can be found, which creates clinically challenging scenarios. Currently, breast cancers with HER2 amplification/overexpression in just over 10% of cancer cells are considered HER2-positive for clinical purposes; however, it is unclear as to whether the HER2-negative components of such tumors would be driven by distinct genetic alterations. Here we sought to characterize the pathologic and genetic features of the HER2-positive and HER2-negative components of breast cancers with heterogeneous HER2 gene amplification and to define the repertoire of potential driver genetic alterations in the HER2-negative components of these cases.ResultsWe separately analyzed the HER2-negative and HER2-positive components of 12 HER2 heterogeneous breast cancers using gene copy number profiling and massively parallel sequencing, and identified potential driver genetic alterations restricted to the HER2-negative cells in each case. In vitro experiments provided functional evidence to suggest that BRF2 and DSN1 overexpression/amplification, and the HER2 I767M mutation may be alterations that compensate for the lack of HER2 amplification in the HER2-negative components of HER2 heterogeneous breast cancers.ConclusionsOur results indicate that even driver genetic alterations, such as HER2 gene amplification, can be heterogeneously distributed within a cancer, and that the HER2-negative components are likely driven by genetic alterations not present in the HER2-positive components, including BRF2 and DSN1 amplification and HER2 somatic mutations.

Electronic supplementary material

The online version of this article (doi:10.1186/s13059-015-0657-6) contains supplementary material, which is available to authorized users.     

Assessing the Pulsatility of Luteinizing Hormone in Female Vervet Monkeys (Chlorocebus aethiops sabaeus)

Specific alterations in the pulsatility of luteinizing hormone (LH) are linked to obesity-related subfertility in ovulatory women. Vervet monkeys (Chlorocebus aethiops sabaeus) are an Old World nonhuman primate that develops obesity and has a menstrual cycle similar to humans. We evaluated follicular-phase LH pulses in 12 adult normal-weight female vervets. Serum was collected every 10 min for 4 h by using a tether device in conscious, freely moving monkeys on menstrual cycle days 2 through 5. Serum estradiol was collected daily during the follicular phase to identify the luteal–follicular transition. For comparison, we used data from 12 ovulatory normal-weight women who had undergone frequent blood sampling of early-follicular LH. LH pulse frequency was similar, with 2.8 ± 0.7 LH pulses during 4 h in vervets compared with 2.3 ± 0.7 LH pulses during 4 h in women. The LH pulse mass (percentage change in the pulse peak over the preceding nadir) was 123.2% ± 27.4% in vervets and 60.9% ± 14.9% in humans. The first day of low serum estradiol after the follicular-phase peak was denoted as the day of the luteal–follicular transition. Luteectomy was performed on luteal days 7 through 9, and corpora lutea were confirmed by histology. We demonstrate that follicular LH patterns in vervets are similar to those in humans and that the luteal phase is easily identified by monitoring daily serum estradiol. These findings demonstrate that vervet monkeys are a suitable animal model for evaluating LH pulse dynamics longitudinally in studies of diet-induced obesity.Abbreviations: CL, corpus luteum; LH, luteinizing hormoneNonhuman primates have been used in biomedical research for decades and have enabled advancements in many areas, including HIV–AIDS, Alzheimer disease, diabetes, asthma, and endometriosis.²³ Neuroendocrine research in menstruating nonhuman primates, such as rhesus and cynomolgus macaques, have provided valuable information regarding the hypothalamic– pituitary–ovarian axis, including modulating factors of pulsatile gonadotropin-releasing hormone secretion and the negative and positive feedback mechanisms of sex steroids.^20,25,33Normal reproductive physiology in women involves highly coordinated communication between the hypothalamus, pituitary gland, and the end organ of female reproduction, the ovary. These processes are governed by the magnitude and frequency of secretory outbursts (pulses) of gonadotropin-releasing hormone from the hypothalamus. The activity of gonadotropin-releasing hormone results in a pulsatile mode of secretion of follicle-stimulating hormone and luteinizing hormone (LH) from the anterior pituitary. In females, follicle-stimulating hormone drives ovarian follicle growth during the follicular phase of the menstrual cycle. The midcycle LH surge results in ovulation and the subsequent formation of a corpus luteum (CL). Secretion of estradiol, produced by the developing follicles, progressively increases over the course of the follicular (proliferative) phase of the menstrual cycle and peaks prior to ovulation. Progesterone, secreted by the CL, is the dominant sex steroid during the luteal (secretory) phase.¹² Both estradiol and progesterone exert tightly regulated negative feedback on the hypothalamus and pituitary and affect gonadotropin release. Alterations in this intricate system can result in anovulation or infertility.Obesity is a growing worldwide hazard that has many adverse health outcomes, including subfertility. Endocrine alterations associated with obesity include relative hypogonadotropic hypogonadism^29,34 and selective impairment of LH pulse amplitude.¹⁴ Progesterone metabolite excretion in morbidly obese women is reduced by 70% compared with that in normal-weight women,²⁹ and pulsatile LH amplitude is suppressed by half in frequent blood-sampling studies.¹⁴ However, despite the recent advances in understanding the endocrine pathophysiology of obesity-related subfertility,¹⁵ its molecular mechanisms are poorly understood.Animal models for obesity-related subfertility are needed for mechanistic studies but are currently unavailable. The hormonal control of the menstrual cycle has been extensively studied in rhesus and cynomolgus macaques and is similar to that of humans.^12,22,26 These nonhuman primates have also been shown to develop obesity and resultant metabolic disturbances.¹ However, demand for rhesus and cynomolgus macaques is high, and the NIH has espoused the need to identify other species of nonhuman primate that are suitable for research.⁶Vervet monkeys (Chlorocebus aethiops sabaeus) are a small, Old World nonhuman primate with an ovarian cycle similar to that in humans; therefore vervets may be an appropriate alternative species in which to do neuroendocrine research. LH pulsatility in this species has not been assessed comprehensively. Our objective in the current study was to characterize the follicular LH pulse pattern in vervet monkeys, to establish the feasibility of using this model in future studies to assess the effect of body mass on pituitary function.